After Takuya Kanbara receives instructions from a cell phone to take a ride on a train unlike our world's, he ends up in the Digital World with three other kids: J. P. Shibayama, Zoe Orimoto, and Tommy Himi, along with two odd Digimon Bokomon and Neemon. Tommy, who was bullied into coming, tries to chase the Trailmon that brought them to the Digital World and comes into danger when he runs out onto the train tracks over open space. Shortly afterwards, Cerberumon attacks at the train station looking for the Human Spirit of Flame. Ultimately Takuya gets the Spirt and Spirit Evolves to Agunimon and fights Cerberumon. Cerberumon is no match for Agunimon and Agunimon destroys him.

While looking for a way back home, J.P. and Tommy run into a lot of Pagumon who chase them down because of J.P.'s chocolate. They fall into an underground labyrinth where Koji Minamoto rescues them, but one Pagumon digivolves into a Raremon. Takuya digivolves to Agunimon, but is suddenly changed back before he can finish Raremon off and knocks Koji down a hole. Koji finds the Human Spirit of Light, Lobomon, and prepares for the true fight. After a battle Lobomon defeats and destroys Raremon and the remaining Pagumon flee. Koji thanks Takuya for saving his life, but is rather rude to him.

On their way to the Forest Terminal, the gang (minus Koji) is ambushed by a large group of Candlemon, who try to fry them. Agunimon isn't even able to stop them with fire, but just when it looks like things are over for him, Tommy's courage to help summons the Human Spirit of Ice, Kumamon. Unfortunately, a Candlemon digivolves to Wizardmon and starts harassing Agunimon and Kumamon. Kumamon is beaten by Wizardmon, but points out which one is the real one to Agunimon and Agunimon defeats him. The Candlemon tribe apologize for the fight as it was a test to see if they were really the Legendary Warriors. With the fractal code taken from Wizardmon, Takuya repairs the bridge for the Forest Terminal.

Takuya, Tommy, Zoe and J.P. follow a rail-road track to the Forest Terminal. The track eventually splits; Zoe and J.P. go left while Takuya and Tommy go right. Zoe and J.P. meet a friendly Flora village full of Floramon who are constantly harassed by the Mushroomon Brothers who have been taken over by evil. In the midst of an argument, Zoe finds her Spirit of Wind and digivolves to Kazemon. A battle begins but Kazemon is eventually defeated when the Mushroomon digivolve to Woodmon but Koji shows up and Spirit evolves to Lobomon. Lobomon defeats Woodmon and purifies him, turning him back into the Mushroomon Brothers who are good again. Woodmon's fractal code turn the Flora village back to normal and the Mushroomon and Floramon are back in harmony. Meanwhile, Tommy and Takuya reach a dead-end and after nearly falling to their deaths, meet up with the others. Both express disbelief at the idea of Zoe getting her Spirit.

The group (minus Koji again) stumble across a wind factory, run by Kokuwamon, Goblimon and Minomon. The group take a tour of the factory hoping to find some food. Later the Kokuwamon tell the group that the Goblimon kidnapped them to work in their factory under the command of an evil Snimon. The group make a plan to destroy the wind factory so the Kokuwamon can be free (minus J.P.; he doesn't have his spirit yet). The plan backfires and the group is almost defeated when J.P. finds his spirit in the heart of the factory and evolves to Beetlemon. Beetlemon defeats Snimon and takes its fractal code. The Kokuwamon are free again. A Minomon reports on what happened to a shadowy figure who is not happy about it.

When looking for food Takuya, Tommy, Zoe and J. P. come across KaratsukiNumemon who ask for their help in exchange for food. They take the challenge and take a train up a cliff to the homes of the KaratsukiNumemon. The group meet up with Koji whilst at the homes and they all try to work together to free the female KaratsukiNumemon. Grumblemon, the evil Legendary Warrior of Earth appears and takes on Agunimon, Lobomon, Kumamon, Kazemon and Beetlemon. Grumblemon then slide evolves to Gigasmon his Beast Warrior form, a previously unseen evolution. Gigasmon proves to be too powerful for the group. Beetlemon attacks Gigasmon but results in the fractal code of the mountain being shown and swallowed by Gigasmon. The group (including Bokomon and Neemon) fall from the cliff and are separated into two groups.

The group is separated from the fall. Takuya, Koji and Tommy in one group and Zoe, J.P., Bokomon and Neemon in another. Takuya's group land on a moving toy island home to WaruMonzaemon, Pandamon and a large group of evil ShadowToyAgumon. Monzaemon Megadramon kidnaps Tommy and Takuya with Koji try to bring him back with the help of Pandamon. Agunimon and Lobomon take on the ShadowToyAgumon as a team and defeat them together and purify them, turning them back into normal ToyAgumon. It turns out Tommy was just playing games with WaruMonzaemon who turned back into his normal Monzaemon form when the ShadowToyAgumon were defeated. As an apology for what they did, the ToyAgumon fly Takuya, Tommy, and Koji to meet the others.

Zoe, J.P., Bokomon and Neemon come across a Digimon School run by a Togemon. One of the pupils, Tsunomon is having a hard time fitting in because he can digivolve to Gabumon. When a flash flood heads straight for the school, Kazemon and Beetlemon make a barrier but Kapurimon is thrown into the water. Tsunomon digivolves to Gabumon to save him and becomes a role model for all the other students. The Tsunomon and Kapurimon students give them a ship to sail over the grass with and they meet up with Takuya, Tommy and Koji who parachute out of the plane to them.

The group (including Koji) reunite and camp in the mysterious TV Forest. They are harassed by an evil Bakumon (corrupted by Cherubimon) which turns Tommy against all the others. Koji digivolves to Lobomon to hold Kumamon off and Takuya digivolves to Agunimon when he spots Bakumon. Bakumon tries to trap him in a nightmare too, but Agunimon frees himself from it and looks like he's about to attack Kumamon, but turns his attack on Bakumon at the last second, defeating him. Agunimon purifies Bakumon back to his normal good self and Tommy returns to normal unaware of what happened. As an apology, Bakumon gives all but Koji, who stays awake, good dreams. Koji gets a message on his D-Tector indicating his Beast Spirit is nearby.

Koji looks for his Beast Spirit with Bokomon and Neemon following. They come across a Gotsumon village, who are terrorised by Grumblemon. Lobomon confronts Grumblemon and a battle ensues. The rest show up and in the fight, Zoe loses her spirit to Gigasmon when she pushed Tommy out of the line of fire. With the help of a Gotsumon, Koji gets his Beast Spirit and he digivolves to KendoGarurumon who Koji can't control. Ultimately both he and Gigasmon fall off a cliff, but Gotsumon saves Koji.

Bokomon takes the group to a fortune telling village to meet Shamanmon. Shamanmon tells the future of the group as Grumblemon shows up with his new hench-digimon, Golemon and traps Koji so he can't evolve to KendoGarurumon. Working together, Agunimon, Beetlemon and Kumamon defeat Golemon, but Tommy loses his spirit to Gigasmon. Shamanmon is possessed by the Beast Spirit of Fire and attacks Golemon, Grumblemon, Agunimon, Beetlemon and the rest. As BurningGreymon, Shamanmon destroys Golemon and drives off Gigasmon. Realizing that BurningGreymon is actually a possessed Shamanmon, Agunimon bravely takes him on alone but is no match for the Beast Warrior. Before he can destroy Agunimon, Shamanmon manages to get enough control to hold himself in place for a moment, allowing Agunimon to defeat him. Agunimon scans BurningGreymon freeing Shamanmon and getting the spirit but with the side effect that he slide evolves into BurningGreymon himself. Takuya also has no control over the Beast Spirit and attacks Beetlemon so the freed Koji evolves to KendoGarurumon to battle him.

Takuya nearly kills Tommy and burns down the forest in his rampage, but Tommy's pleas and tears hitting BurningGreymon's eyes cause Takuya to regain control over himself and de-digivolve leaving him afraid of using his Beast Spirit again. Grumblemon attacks and traps the others and takes Tommy. Takuya, still scared of his Beast Spirit, digivolves to Agunimon instead of BurningGreymon but is no match for Gigasmon and is defeated. Desperate to save Tommy, Takuya takes a chance and digivolves to BurningGreymon and is in complete control this time. He rescues Tommy then turns back into Agunimon to lure Gigasmon out of the forest to stop it from burning down in the fight and into the open before turning back into BurningGreymon. As they're on a wide-open plain, Gigasmon has the advantage as he's the Warrior of Earth, but BurningGreymon is more powerful and doesn't have to worry about burning down the forest and BurningGreymon finally defeats Gigasmon. He takes Gigasmon's Beast Spirit and retrieves Tommy's human one, but before he can get Zoe's back, Gigasmon turns back into Grumblemon who runs away. Ranamon, Mercurymon, Arbormon and Duskmon appear as the remaining Legendary Warriors.

The group makes it to the Forest Terminal and encounter Sorcerymon who leads them to a frozen Seraphimon. Seraphimon springs to life and tells of the prophecy of the Legendary Warriors and how he was frozen. It is revealed that the other good Celestial Digimon Ophanimon is the one who has been contacting the DigiDestined and leading them to this point. Mercurymon, Arbormon, Ranamon and Grumblemon arrive and fight Seraphimon. During the battle that follows, Mercurymon reflects Seraphimon's attack and destroys him, taking his Fractal Code. The DigiDestined escape with Seraphimon's egg with the sacrifice of Sorcerymon. They are now heading out to find Ophanimon.

Trailmon takes the kids to an underwater cave where they meet a Whamon who was stuck there due to the likes of Grumblemon. Grumblemon shows up with Arbotmon who turns into Petaldramon and a bunch of Golemon. Agunimon, Lobomon, Kumamon and Beetlemon take out most of the Golemon and battle Petaldramon, but J.P. is too injured to fight although he tries and with Kumamon's help destroys all but one Golemon. J.P's defeated by the last Golemon and Grumblemon goes to kill him, but stopped by Whamon who blasts him away, temporarily defeating him. Whamon's attack also releases J.P.'s Beast Spirit which he'd accidentally swallowed and he takes it and digivolves to MetalKabuterimon. MetalKabuterimon is unable to control himself and brings the cave down on them, defeating Petaldramon, but he manages to regain control and turns his attention to Grumblemon. With one shot, MetalKabuterimon destroys Grumblemon and the last Golemon and as Beetlemon he takes Grumblemon's remaining Spirit and returns Zoe's to her. With Grumblemon destroyed and Arbormon defeated, the kids escape in Whamon as the cave floods.

The group end up on an island paradise ran by four Toucanmon who are also members of Ranamon's fan club. The Toucanmon steal the boys D-Tectors with Zoe the only one who manages to keep hers due to her noticing the Toucanmon and drawing the attention of the others. As the group chases the Toucanmon, Ranamon shows up and Zoe evolves to Kazemon to fight her. Kazemon is no match for Ranamon and things get worse when Ranamon finds her Beast Spirit and evolves into Calmaramon. Her ugliness scares off the Toucanmon and Kazemon is no match for her, but when Calmaramon uses her "Titanic Tempest" attack, she loses control of her Beast Spirit and flies away. The group discovers the Toucanmon gone and quickly chase after them to get their D-Tectors back.

The Toucanmon, with the boys D-Tectors fly to Island. When trying to make it to the Goma island, the group is stopped by Gomamon. The tell them of the dangerous whirlpools blocking the island. Determined to make it to the island and return the home, the group builds a raft to try to sail around the whirlpools, but Ranamon arrives having apparently gotten full control of her Beast Spirit after extensive (and destructive) training. Zoe evolves to Kazemon, but is once again no match for Ranamon and is knocked into the whirlpools where Zoe finds her Beast Spirit which was causing the whirlpools. Zoe evolves into Zephyrmon and unlike the boys, is in complete control of herself. Ranamon is no match for Zephyrmon so she evolves into Calmaramon who gets the better of Zephyrmon. Insulting Calmaramon, the boys distract her long enough for Zephyrmon to get free and retaliate. Calmaramon tries her "Titanic Tempest" attack, but again loses control of her Beast Spirit and flies away again. The DigiDestined and the Gomamon make it to Goma Island where the celebrate finally being home, but reveal that the Toucanmon have left for the Autumn Leaf Fair on a nearby continent to sell the D-Tectors.

The group make it to the Autumn Leaf Fair on their raft and look for the D-Tectors. Tommy finds a Datamon with them and can get them when he trades him something after he earns Datamon's sympathy and wins a game for him. Tommy locates the Toucanmon and takes the camera they traded for the D-Tectors, but after he saves their lives, they take the camera back and run off. Arbormon tries to use the camera to trade for the D-Tectors, but after he sees what Tommy did thanks to the camera recording it, Datamon refuses and decides to give them to Tommy instead as he deserves them. Arbormon digivolves to Petaldramon and attacks, but Takuya and Koji hold him off while Datamon gives Tommy back his D-Tector and reveals he programmed his Beast Spirit of Ice into it which was the prize of the game he had earlier won. With his D-Tector returned to him along with his new Beast Spirit, Tommy digivolves to Korikakumon to do battle. Korikakumon battles Petaldramon and is able to hold his own, but Tommy lacks full control of his Beast Spirit and is trapped by Petaldramon's Thorn Jab. Datamon gives Takuya and Koji back their D-Tectors and they digivolve to Agunimon and Lobomon who free Korikakumon. After being freed, Korikakumon sends Petaldramon skidding far away with his Frozen Arrowheads. A message from Ophanimon comes to them now that they've got all of the Beast Spirits offering them one last chance to go home. When they refuse, she tells them to go to the Rose Morning Star and they start their journey on a Trailmon using tickets Zoe won in an eating contest.

A Trailmon race is about to begin but due to the appearance of ShadowWereGarurumon and Dogmon the other Trailmon don't have partners. Takuya, Zoe, Tommy, Koji, J.P. and Neemon jump on the Trailmon as replacements. Neemon is automatically disqualified due to him falling asleep at the starting line with his Trailmon following him. Raccoon Dog and J.P. are eliminated from the race because of a Raremon. Due to the foul play of ShadowWereGarurumon and Dogmon, Zoe, Tommy and Koji are eliminated from the race and even Takuya digivolving to Agunimon to fight ShadowWereGarurumon isn't enough to stop them. After getting trapped in a tunnel with Takuya's Trailmon Worm's fuel set on fire, Takuya digivolves to BurningGreymon and drags Worm out of the tunnel. BurningGreymon fires his Wildfire Tsunami into Worm who uses it to breathe fire on ShadowWereGarurumon and Dogmon's Trailmon, Buffalo, defeating it and them. BurningGreymon de-digivolves to Takuya and he and Worm win the race. As their prize, the kids win a free trip to Burgermon Village.

Petaldramon raids the Burgermon village with Chamelmon and captures the best cook in the village. The Group try to save him by making the perfect burger and Tommy makes a good start so the Chamelmon kidnap him, Zoe and J.P. while inside Takuya and Koji remain oblivious as they compete to find who makes the best burger, forcing Bokomon and Neemon to test their awful creations. At Petaldramon's mansion, PapaBurgermon is forced to work as his children have been captured and Tommy, J.P. and Zoe help him. They run out of time and digivolve to Kumamon, Beetlemon and Kazemon to fight the Chamelmon. With the help of the Burgermon kids, they trap the Chamelmon and Kumamon defeats them with his Crystal Freeze attack. Kumamon performs his first Fractal Code Digitize, de-digivolving the Chamelmon to Armadillomon and forcing them to run. This buys PapaBurgermon enough time to finish the perfect burger, but Petaldramon arrives before he can finish and the kids Beast Spirit evolve to fight him. PapaBurgermon finishes the burgers and feeds Petaldramon who cuts the fight short to eat and sleep afterwards. The kids and the Burgermon escape and outside, MetalKabuterimon destroys Petaldramon's manison. Tommy, JP and Zoe return the Burgermon home where PapaBurgermon names his new creation the Little Tommy after Tommy. At Petaldramon's ruined manision, Petaldramon wakes up hungry, but decides to go back to sleep instead of attacking again.

Traveling towards the Rose Morning Star, the group is thrown out of their Trailmon outside the Continent of Darkness as the Trailmon is afraid of it and even Bokomon doesn't have any information on it. In the darkness, everything is initially scary to the group, but after they find out everything is actually not so bad, they cheer up. At the same time, Cherubimon's Evil Legendary Warriors are visited by Cherubimon himself and they turn over the Fractal Code they have collected, except for Seraphimon's. Cherubimon is aware of this, but allows Mercurymon to keep it for now and sends Arbormon to destroy the kids. Duskmon confronts Mercurymon who he has figured out wants to rule himself and is using the others to do his dirty work until the right time comes to strike. Duskmon considers getting involved in the fights for once. Arbormon suddenly attacks the group, destroying some nearby Pipismon and evolving into Petaldramon. The kids Beast Spirit evolve, but Petaldramon eats a tree and grows to giant size, becoming more than a match for the group. Finally, with some teamwork, they manage to overpower Petaldramon and a combined attack from BurningGreymon and Zephyrmon finishes him. Lobomon gets his Beast Spirit and they give Arbormon the chance to surrender. However, Duskmon shows up and destroys Arbormon as he is now useless without his Beast Spirit and prepares to confront the Legendary Warriors himself.

Duskmon defeats all Legendary Warriors with most in their Beast Spirit forms so they decide to regroup and plan out their attack. Takuya gets cocky and believes they are unstoppable despite Koji's warnings. In the battle that follows, Takuya as Agunimon tries to restrain Duskmon and allow the others in their Beast forms to defeat them, but the attack fails. Agunimon is nearly killed, but KendoGarurumon leaps in and takes the blow and is seriously wounded. Seeing Koji badly hurt, Duskmon screams out in anguish and releases a dark cloud. Despondent, Takuya hops on a Trailmon and returns home.

Feeling sad, Takuya returns home but finds himself in the past on the day he first came to the Digital World. Due to his broken spirit, he returns as a Digimon, Flamemon and is haunted by an image of Duskmon. Realizing he has a chance to change his destiny and believing the others will be better without him, Takuya follows his past self to try to convince him not to get on the Trailmon. While following himself, he spots a boy who looks like and is following Koji, but doesn't investigate. Given the chance to stop himself, Takuya realizes his friends and the Digital World needs him and screams at himself to go. He regains his spirit and destroys the image of Duskmon that has been haunting him. Dark Trailmon returns and offers Takuya a ride back to the Digital World but warns that it will be a one-way trip. Takuya accepts this and returns to the Digital World, evolving back into Agunimon on the way.

Takuya returns to the digital world as Agunimon but finds only a crater where the last battle with Duskmon took place and no sign of the others. Eventually he finds and rescues Bokomon and Neemon from a Sepikmon who is trying to make friends in the wrong way and learns that all but Koji have been captured by Mercurymon and Ranamon. As a gesture of friendship, Sepkimon uses his boomerang to guide the three to their friends who are being tickle tortured to give up their Spirits. Koji evolves to Lobomon to free them, but is no match for Ranamon and Mercurymon. Agunimon arrives and with his senses sharpened so that he can sense changes in the weather, he picks the perfect opportunity and saves his friends. Amplifying their various powers with that of a storm that rages, the group drives off Mercurymon and Ranamon and Takuya is hailed as a hero for his rescue of them with the group noticing his changes. However, Mercurymon claims to have a new plan that will defeat them.

Working their way to the Rose Morning Star, J.P. tries to take the lead to the amusement of the group. All but Bokomon and Neemon are suddenly sucked up into a giant structure made of ten orbs, the Beast Warrior of Steel, Sakkakumon. Inside Sakkakumon J.P is pushed into a portal into the Sphere of Earth where he is confronted by Volcamon who prays on his fears about his friends not really being his friends. J.P. evolves to Beetlemon and destroys Volcamon, but is confronted by an evil version of his own shadow which takes on physical form and continues to pray on his fears by creating evil clones of the group who yell bad things at Beetlemon. He becomes MetalKabuterimon when he can't defeat his shadow, but his shadow follows and has the upper hand until MetalKabuterimon realizes that his friends really are his friends when they come to support him and he blasts his shadow at point-blank range, destroying it. Just as the group is finally reunited, they are shoved into various portals and separated.

In the Fire Sphere, Tommy is confronted by an evil Digimon but is saved by a mysterious cloaked stranger, Asuramon who claims to be his friend. However, Asuramon's ideals of friendship clash with what Tommy has learned from being friends with the others and he remembers what his brother, who was trying to keep him from becoming a spoiled brat tried to teach him and he realizes that Asuramon is wrong. Asuramon reveals himself as the Digimon that attacked Tommy before and that all he really wanted was his Spirits. Tommy evolves to Kumamon, but is no match for Asuramon. Kumamon manages to knock Asuramon into the lava, but when he emerges again, Kumamon evolves into Korikakumon and destroys Asuramon. Tommy finally understands what true friendship is and thanks his brother as he leaves Sakkakumon and is reunited with Bokomon and Neemon. In the Wind Sphere, Koji encounters Karatenmon. Karatenmon is able to read his heart and makes fun of him for denying himself friends saying it makes him weak. Koji believes it is just prudent because everyone eventually leaves you and Karatenmon has a revelation about Koji's mother causing him to feel this way. Koji evolves to Lobomon, but is no match for Karatenmon who can read his heart and can predict his every move. However, when Lobomon evolves to KendoGarurumon, he is too fast for Karatenmon and destroys him.

Zoe is stuck in the Water Sphere, where she has a flashback about being teased and finding a new friend. Inside the Sphere with her are three Honeybeemon and Ranamon who they worship. Believing Zoe to be evil, the Honeybeemon set various traps for her, but fall into them all and Zoe has to rescue them each time. She earns their friendship in doing so, but a jealous Ranamon has the Honeybeemon give her a poisoned apple to make her hallucinate and remember how she was picked on and her new friend turned against her rather than stand up for her. However, this just increases Zoe's desire to be a better friend in the future and when Ranamon insults her, Zoe snaps out of it and evolves to Kazemon to fight. Kazemon is no match for Ranamon so she evolves into Zephyrmon with Ranamon following suit into Calmaramon. Unlike their previous fights, Ranamon has full control of her Beast Spirit and beats up Zephyrmon. However, the Honeybeemon switch sides due to Zoe's goodness and with their encouragement, Zephyrmon beats Calmaramon and finally destroys Ranamon. With Ranamon destroyed, Zoe and the Honeybeemon escape Sakkakumon. In the Wood Sphere, a hungry J.P. is attacked by a Cherrymon. J.P. quickly evolves into Beetlemon and easily destroys Cherrymon, freeing him from Sakkakumon where he later reunites with Zoe as well as Tommy, Bokomon and Neemon. In the Thunder Sphere, Takuya is confronted by Parrotmon. Takuya quickly evolves to Agunimon and effortlessly destroys Parrotmon.

Realizing that Takuya and Koji are still stuck inside Sakkakumon, J.P., Zoe and Tommy spirit evolve and try to break back in, but are unsuccessful. However, Duskmon, wanting to find out why he reacted to Koji's pain as he did, manages to break into the Darkness Sphere to confront Koji. Realizing he's in trouble, the group tries to contact Takuya and Koji through their D-Tectors and manage to get through to Takuya. They explain that he is stuck inside Sakkakumon, the Beast Warrior of Steel and that the only way out is to defeat the opponents he comes across, but that Koji is in trouble. Takuya faces off against IceLeomon in the Ice Sphere and manages to destroy him as Agunimon after a fight, but chooses to look for Koji rather than escape. In the Darkness Sphere, Duskmon confronts Koji and shifts through his memories of his life, learning that Koji's mother is dead and that he is distant from his step-mother. On the day he entered the Digital World, he was buying flowers for his step-mother to try to make it up to her when Ophanimon contacted him. Koji realizes just how mean he is to her and swears that when he returns to the human world he will make it up to her. Koji evolves to Lobomon and then KendoGarurumon but is unable to defeat Duskmon and is defeated. Before Duskmon can kill him, Serpahimon's Digi-Egg reacts and gives him the power to Fusion Evolve into Beowolfmon who is a match for Duskmon. During the fight, both of their true forms are briefly revealed and it is shown that Duskmon is actually the boy who looks like Koji that Takuya had briefly seen on his return to the human world. Their fight causes an explosion that blows them out of Sakkakumon just before Agunimon reaches them.

Making his way through Sakkakumon, Agunimon enters the Steel Sphere where he is confronted by a manifestation of Mercurymon himself. In the Steel Sphere which is Mercurymon's element and with Mercurymon able to reflect attacks and manifest himself in any mirror, Agunimon is no match for him and follows him to the Light Sphere where Mercurymon is keeping Seraphimon's Fractal Code. Mercurymon uses the Fractal Code to evolve into ShadowSeraphimon and easily defeats both Agunimon and BurningGreymon. As the others desperately try to get back in again, Bokomon's pleas cause Seraphimon's Digi-Egg to give Takuya the power to Fusion Evolve to Aldamon. As Aldamon, Takuya is more than a match for ShadowSeraphimon and he retrieves Seraphimon's Fractal Code and returns it to his Digi-Egg. Aldamon follows Mercurymon back to the Steel Sphere where he easily defeats him and collects the Human Spirit of Steel, though Mercurymon survives in the form of Sakkakumon. Exiting Sakkakumon, Takuya reunites with the others in time for Seraphimon's egg to hatch as Patamon.

When they think Mercurymon is defeated, he returns in his Beast Spirit form, Sakkakumon. They attack him but he just shoots their attacks back at them. Aldamon, Kazemon, Kumamon and Beetlemon are forced to run with Bokomon, Neemon and the newly born Patamon. Sakkakumon uses their fears against them and everyone but Aldamon fights each other out of fear until Aldamon breaks it up. Using their Digimon senses and combining their attacks, they are able to hurt Sakkakumon a bit as he never saw combined attacks before. Realizing that Sakkakumon's central sphere, the Sphere of Darkness, never moves and never attacks them, Aldamon has Kazemon, Kumamon and Beetlemon attack Sakkakumon together, stopping the movement of the spheres. Aldamon attacks the central sphere with his Atomic Inferno attack while the spheres are stopped and Sakkakumon is destroyed. Aldamon gets his Beast Spirit and with Sakkakumon (and consequently Mercurymon) finally destroyed, Duskmon is the only evil Legendary Warrior left.

As Duskmon and Beowolfmon continue to fight, Patamon leads the rest of the gang to Koji but Cherubimon traps them. Eventually they manage to escape by digging their way out. As Duskmon is losing, Cherubimon intervenes and gives him the Beast Spirit of Darkness, allowing him to evolve into Velgemon. Velgemon is more than a match for Beowolfmon and defeats him, with Koji barley escaping an attack that would've killed him. Before Velgemon can finish him off, Ophanimon intervenes through Koji's D-Tector and reminds Velgemon of his life in the human world: he is actually Koji's long-lost twin brother Koichi who found out he had a brother not long before from his dying grandmother. He followed Koji to the train station but missed the elevator and ended up falling down the stairs before somehow ending up in the Digital World. Confused, Velgemon flies off, leaving Koji alone.

After the gang finally get back together again Koji decides to run off after Duskmon to find out their connection and Takuya chases after him. Instead of waiting for Takuya to return with Koji, J.P. decides to look for a Digimon that knows something about the Rose Morning Star and in a Trailmon Graveyard, they find a dying Trailmon named Angler who claims to know something but holds it over their heads to force them to do things for him. Eventually he confesses that he just wants friends and they happily help him though they don't actually believe he knows anything. Angler apparently dies, but is instead renewed. Angered at being tricked, the group Beast Spirit evolve to beat him up, but decide that Angler is too pathetic to bother with. Giving them a ride to find the others, Angler reveals what he knows: shortly after the battle between the three Celestial Digimon, Angler was forced by the Evil Legendary Warriors to carry a container to a castle at the Rose Morning Star. Given the timing, Angler always believed it contained either Ophanimon or Seraphimon. The group realizes it has to be Ophanimon as Seraphimon is now Patamon and are excited as they are now close to the Rose Morning Star and finally meeting Ophanimon in person.

As he now knows Koji is his brother, Duskmon doesn't want to fight him anymore, but Cherubimon takes advantage of his restored memories to prey on Duskmon's anger at Koji and his father for abandoning their mother who is sick and has to work hard to increase his control over him. Duskmon confronts Koji as Beowolfmon and finally reveals the truth to Koji, that he is his twin brother. Duskmon defeats Beowolfmon and as Velgemon nearly kills Koji, but Takuya saves his life. While Patamon distracts Velgemon, Koji reveals what he has learned to Takuya who insists a reluctant Koji fight as he is the only chance his brother has. Koji refuses so Takuya evolves to Aldamon to fight on his own, but is no match for Velgemon. Koji finally steps up to fight, evolving to Beowolfmon and teaming with Aldamon against Velgemon. Aldamon manages to weaken Velgemon with an attack, allowing Beowolfmon to finally defeat him. Koji purifies the Spirits of Darkness, releasing Koichi just as the others catch up to them on Angler. Takuya is shocked as he recognizes Koichi from his brief return home.

Koichi is released from the form of Velgemon and explains that he is Koji's twin and his backstory. Out of guilt for what he has done, Koichi remains distant from the group as they travel on Angler to the Rose Morning Star. On the way, Cherubimon attacks and Aldamon, Beowolfmon, Beetlemon, Korikakumon and Zephyrmon are unable to defeat him and are defeated themselves. Cherubimon offers Koichi the chance to rejoin him, explaining that the Spirits of Darkness chose him because of the darkness in his heart after rejecting many other Digimon. Koichi refuses to let darkness control him anymore, causing him to get a D-Tector and the Spirits of Darkness to become the true Spirits of Darkness. Evolving to Löwemon and JägerLöwemon, Koichi proves more than a match for Cherubimon and destroys him, but it turns out to just be a projection, not the real Cherubimon who promises to see the group at the Rose Morning Star. Koichi initially intends to go on alone, but the group refuse and join him despite the dangers.

The gang finally arrives at the Rose Morning Star where they find a castle where data is being drawn to it. All Koichi knows is that Cherubimon is collecting data for an unknown reason and the group spirit evolves to make their way into the castle. At the gate, they are attacked by two Phantomon and all but Löwemon are captured. Löwemon manages to avoid the Phantomon's attacks and destroy them, freeing the others. Making their way into the castle, they come under attack by mysterious shadows coming from mirrors, but are saved by Oryxmon. The group is initially wary of him despite his promises to take them to Ophanimon until Patamon announces that he is good. Oryxmon leads the group to an imprisoned Ophanimon who explains the events leading up to this: there was a war between Human and Beast Digimon that was stopped when Lucemon came and brought peace to the Digital World until he was corrupted by his own power. The Ten Ancient Warriors defeated him and disappeared, leaving behind two Spirits each and the three Celestial Digimon, Seraphimon, Ophanimon and Cherubimon to rule the Digital World. Cherubimon had different beliefs than Serpahimon and Ophanimon and was eventually corrupted by jealousy and evil, becoming a monster. He led an army of Beast Digimon against his two former friends and seriously wounded Seraphimon, causing Ophanimon to sacrifice herself to Cherubimon's custody to save him. Cherubimon then created the Evil Legendary Warriors and sent them and evil Digimon out into the world to gather data and cause chaos, causing Ophanimon to call for children from the human world to come and bring peace back to the digital one. Ophanimon tells them that with the power of the Ten Legendary Warriors they must now defeat Cherubimon who shows up himself and tells them that them coming there was all part of his plan to gain their Spirits in order to use them and the data he is collecting to take over the Digital World. As Cherubimon gloats, the Spirits start reacting, making the kids nervous.

Pleased with the fact that everyone is now there, Cherubimon destroys Oryxmon as his usefulness has come to an end. He reveals to a shocked Lwemon that he was just using him the whole time he was Duskmon to make sure that all of the Spirits arrived at his castle so he can get ultimate power. Löwemon attacks Cherubimon, but as they are in a room full of light with no darkness, his power is weakened and he has no effect on Cherubimon who attacks him back so Takuya and Koji quickly evolve to Aldamon and Beowolfmon. Unfortunately their attacks don't work due to the great light so they take the fight outside while the others work on freeing Ophanimon. As Aldamon and Beowolfmon hold off Cherubimon, Beetlemon, Löwemon, Kumamon and Zephyrmon work on breaking the mirrors reflecting the light beams in order to free Ophanimon. Ultimately Aldamon and Beowolfmon are defeated and Cherubimon gets Takuya and Koji's D-Tectors. He then proceeds to attack the others, getting all of theirs until only Zephyrmon is left. At the last moment, Ophanimon breaks free and saves Zephyrmon who is devolved to Zoe. Ophanimon faces Cherubimon and apparently purifies him, but in reality steals back the D-Tectors while he is distracted and gives them back to the kids before teleporting them outside. Ophanimon blasts Cherubimon onto a cliff edge, but contacts the group through Takuya's D-Tector to tell them that she failed and that they must combine their Spirits to defeat Cherubimon. With the last of her power, Ophanimon evolves Takuya and Koji's D-Tectors before becoming a Digi-Egg. Realizing what Ophanimon means, the group quickly splits all of the Spirits, including their own, between Takuya and Koji, allowing them to evolve into EmperorGreymon and MagnaGarurumon who prepare to fight a recovered Cherubimon.

Takuya and Koji evolve to EmperorGreymon and MagnaGarurumon and battle Cherubimon after getting their friends to safety on Cherubimon's castle. Eventually they defeat him, but he disappears and his castle is destroyed. Koichi nearly falls to his death during the escape, but is saved by MagnaGarurumon. While the group is wondering what to do next, an IceDevimon arrives that according to Bokomon went on a rampage across the Digital World, killing Digimon and absorbing their data. Eventually an army defeated him, but he was too powerful for even Cherubimon to kill so he was imprisoned beneath his castle and escaped when it was destroyed. He quickly freezes Takuya and Koji's D-Tectors so they can't fight and engages the others who spirit evolve to fight him. IceDevimon proves too powerful for the group and traps Kazemon and Beetlemon. Kumamon and Löwemon evolve into Korikakumon and JägerLöwemon, but are unable to defeat him and he traps Takuya and Koji in a bubble in which they slowly freeze. JägerLöwemon frees them and has Korikakumon free the others. Beetlemon and Kazemon quickly evolve into MetalKabuterimon and Zephyrmon and Korikakumon and Zephyrmon use their wind and ice to freeze IceDevimon, holding him in place while MetalKabuterimon blasts him, cracking and weakening him. With IceDevimon weakened, JägerLöwemon is able to destroy him and turn back into Löwemon to purify him. With IceDevimon gone, Takuya and Koji's D-Tectors return to normal and Koichi is accepted as a full member of the group. However, Cherubimon is revealed not to be dead and still collecting data to himself in the ruins of his castle, causing them to realize that it is not over yet.

More data streams to the top of the ruins of Cherubimon's castle before stopping. However, it affects the gravity of the area. Realizing that they still need to stop Cherubimon and that this could be their last battle, Takuya and Koji evolve back into EmperorGreymon and MagnaGarurumon and make their way to the castle to finish the fight. Cherubimon compresses all of the data he has gathered into an orb and puts it into his forehead, increasing his power. MagnaGarurumon distracts him, allowing EmperorGreymon to launch a massive attack upon Cherubimon, destroying most of his body. However, with all of the data he has inside of him, he is able to regenerate and grow to a massive size. Cherubimon is easily able to defeat EmperorGreymon and MagnaGarurumon, knocking them out for a minute, but they recover. Following MagnaGarurumon's idea, they charge Cherubimon with MagnaGarurumon absorbing all of his attacks to allow EmperorGreymon in close to attack his forehead with his sword. MagnaGarurumon eventually falls, but EmperorGreymon reaches Cherubimon and stabs him in the head, mortally wounding him and releasing the compressed data. EmperorGreymon purifies Cherubimon who reverts back into his old good self and dies, crying after seeing the spirits of Seraphimon and Ophanimon. Takuya and Koji reunite with the others and celebrate the win which seems like the end, but it is revealed that it is not: the data released from Cherubimon travels to the Dark Area in the core of the Digital World and dissolves part of the seal keeping in Lucemon who releases the Royal Knights to pick up where Cherubimon left off and release him from his imprisonment through the data of the Digital World.

Everyone celebrates what seems like the final battle, but Koji is confused as to why the land hasn't been restored after the data was taken from Cherubimon. Suddenly a nearby mountain range is scanned and everyone rushes off to investigate but comes under attack by Baromon. When they spirit evolve, he stops the attack and reveals that Lucemon is returning and the Digital World still needs their help. Baromon takes the group to the Tunnel of History where he shows them what has led up to this point: when Lucemon was corrupted the Ten Ancient Warriors stopped him, sealing him in the Dark Area at the core of the Digital World. They then split into the Spirits which were split up among the three Celestial Digimon. Lucemon bided his time and eventually used his aura to corrupt Cherubimon and used him to gather the data of the Digital World so he could be released. When Cherubimon was destroyed, that data was absorbed by Lucemon. Through two new minions that Baromon is unable to identify, Lucemon is continuing his work and Baronmon prophesizes that he will return. While Baromon wants the kids to return to the human world, they refuse, wanting to stay and stop the return of Lucemon even if it means they have to defeat Lucemon himself. As they discuss things, the two evil Digimon scan the Tunnel of History and they are forced to flee to the surface. There they confront the Digimon who reveal themselves to be the Royal Knights, Dynasmon and Crusadermon who used to protect the Digital World but now serve Lucemon. The group quickly evolves to Aldamon, Beowolfmon, Kumamon, Kazemon, Beetlemon and Löwemon and take on the two, but have no effect on them even after evolving to their Beast forms and are easily defeated. Takuya and Koji evolve into EmperorGreymon and MagnaGarurumon but even their most powerful attacks have no effect on the Royal Knights and they are defeated. When Baromon tries to attack, the Knights send a wave of energy at him and the kids, but Baromon takes the attack for them and is destroyed while all the kids except Koichi's Fractal Code is revealed. EmperorGreymon and MagnaGarurumon again try to stop them before they can kill their friends, but Dynasmon launches his "Breath of Wyvern" attack which is so powerful it blows the group to the moon while Lucemon demands his servants collect more data for him.

Dynasmon's attack creates a warp that pushes the group to the Digital World's Blue Moon where all but Koichi are left injured and unconscious. Koichi locates some Starmon that take them to their base and help the others recover from their injuries. In the Digital World, Dynasmon and Crusadermon rapidly scan various areas and send their data to Lucemon, drawing ever closer to freeing him and his promise of helping them reach the human world so they can rule it. The gang tries many different methods to reach the Digital World, but fail, learning that there is an electromagnetic stream blocking them from getting back there. With the help of the Starmon and some Burgermon who are friends with the Burgermon they helped previously, they launch themselves in a rocket to the Digital World at the one point in time when the Electromagnetic Stream can be crossed. They don't have enough speed so Takuya evolves to BurningGreymon and pushes them through the stream. On the other side, they land on a Trailmon track and a Trailmon named Mole agrees to push them the rest of the way back.

Dynasmon and Crusadermon scan another area and decide to head to the nearby Steel Town to get the data there. In Steel Town, the gang arrives back in the Digital World on Mole and while making their way into town, are confronted by Sagittarimon who wants their possessions, but keeps getting confused with the word obsessions. Before the kids can spirit evolve and deal with him, four more kids, Katsuharu, Teppei, Teruo and Chaki arrive with an Angemon who scares off Sagittarimon. Tommy is unhappy to see them as he recognizes Katsuharu and Teppei as two kids who bully him and pushed him onto the Trailmon to the Digital World. The new kids explain that they were among the other kids Ophanimon called to the Digital World, but stayed when she sent everyone home and have been traveling with Angemon who protects them while having adventures. The gang tries to convince the other kids to go home, but they refuse. Angemon explains that Ophanimon assigned him to protect the kids when they refused to leave and they refuse to listen even to him about going home. Teppei tries to bully Tommy into forcing the main group to leave instead, but Katsuharu stops him, though he continues to pick on Tommy who finally stands up for himself to the two. Before things can go further, Sagittarimon returns with an army of Centarumon and attacks. Angemon holds them off by himself, but a group sneak around and go after them from the side. When Teppei is in trouble, Katsuharu freezes, but Tommy saves his life then evolves to Korikakumon to protect Katsuharu and his friends. The others quickly evolve as well and Agunimon, Lobomon, Löwemon, Kazemon, Beetlemon and Korkikaumon drive off the army while Angemon defeats Sagittarimon. Recognizing Tommy's bravery, Katsuharu makes peace with and befriends Tommy and decides it is time for his group to return home. However, the Royal Knights arrive, kill Angemon and kidnap Katsuharu's group. Tommy grabs onto their net and follows them as they leave.

The Royal Knights take Katsuharu, his friends and Tommy to a village called Beanstalk Village that has a giant beanstalk in the middle. Dynasmon demands the location of a key, but the kids don't know what he's talking about so he locks them up with the villagers, the Mamemon. The Mamemon Elder explains that Katsuharu and his friends had previously visited and the Mamemon shared their food with them despite not having much. As a gesture of their friendship, the kids planted the Mamemon's last bean for them and it grew into the giant beanstalk. The beanstalk prevents the Royal Knights from scanning the land and they need the key to getting rid of the beanstalk to get the data. They kidnapped the kids because they believe they know where it is. Meanwhile, Takuya and the others are warned not to go to Beanstalk Village by scared Trailmon, but they hitch a ride on Worm when he tries to take off without them. They find the tracks broken and start using tracks from behind Worm to fix them with Takuya's determination to save the Digital World renewing Worm's spirit. At the village, Tommy and the others get free but are attacked by the Royal Knights who kidnap the Elder and tie up Tommy. Crusadermon tries to scan Katsuharu's Fractal Code, but he is saved when the others arrive. Takuya and Koji quickly evolve to EmperorGreymon and MagnaGarurumon, but their attacks have no effect on the Royal Knights and Koichi is taken hostage. The Mamemon attack, allowing MagnaGarurumon to rescue Koichi, but Dynasmon and Crusadermon beat up EmperorGreymon and MagnaGarurumon. Before they can be killed, the Mamemon Elder reveals that the key is a golden bean pod at the top of the beanstalk. The Knights destroy it and with it gone, they are able to scan the entire area while the Mamemon, kids, Bokomon, Neemon and Patamon escape on Worm. Katsuharu offers to take the Mamemon back to the human world, but they refuse to go and reveal they have another bean to plant to create a new beanstalk. Katsuharu and his friends return home on Worm, but not before Katsuharu has Tommy shove him onto the Trailmon so they are even from when he shoved Tommy on to enter the Digital World.

Traveling through what's left of the Digital World on a Trailmon, the gang comes across the Village of Beginnings where all Digimon are born and reborn. There they meet Swanmon, the caretaker and learn that she has to take care of all of the babies born because the Trailmon are too scared to transport them to their families. After reminiscing about their families and being part-Digimon now, the gang go to try to convince the Trailmon to transport the babies but fail. They return to find that the Royal Knights have arrived to scan the Village and explain that Lucemon now plans to populate the world with clones he can control. Takuya and Koji quickly evolve to EmperorGreymon and MagnaGarurumon to do battle but don't fight as they are scared of hurting the eggs. While the others gather the eggs, Zoe goes to the Trailmon again and convinces them to help. EmperorGreymon and MagnaGarurumon are quickly beaten and revert to Takuya and Koji. Dynasmon tries to use his "Breath of Wyvern" attack to finish them, but the babies are able to destroy the attack with a combined attack of their own. Before anymore can happen, the purified Spirits of the other Warriors travel to their Digi-Eggs and take physical form to help fight. The kids quickly spirit evolve to their Human Warrior forms and the Ten Legendary Warriors work together to defend the Village of Beginnings. Together, they are too powerful for Dynasmon and Crusadermon and the Royal Knights retreat, but Dynasmon scans the Village as he leaves and sends the data to Lucemon. The other Warriors return to their egg state while their Spirits return to Takuya and Koji. While they failed to save the Village, the battle allowed Bokomon, Neemon, Patamon and Swanmon enough time to get all of the eggs and babies loaded on the Trailmon who take them home. While they have lost again, Takuya is determined that they will find a way to win and restore the world.

The kids worry about their chances of winning since even with the Ten Legendary Warriors together, they were unable to defeat Dynasmon and Crusadermon. Worrying about what to do next, a bunch of Poyomon arrive and warn that the Village of Flames, Bokomon and Neemon's home and where they started their journey is under attack by Lucemon's servants. Catching a ride on a passing Angler Trailmon, they quickly head back to the Village to save it. Near the Village, a SkullSatamon forces a Palmon and Gajimon to tell him where to find the data for the forest so he can scan it, then kills him and the other Digimon who had refused to tell him while an impatient Lucemon tells the Royal Knights to aid his servants in scanning the data of the world. The group arrives, happy to find the Village still in one piece, but witness SkullSatamon scanning the forest and sending the data to Lucemon. The inhabitants lose faith in the kids, but they rally them to defend their home so SkullSatamon awakens his brother to help. This scares off the inhabitants, but Takuya and Koji evolve to EmperorGreymon and MagnaGarurumon to do battle. The two easily beat the two SkullSatamon, but they summon a third brother and together are too much for EmperorGreymon and MagnaGarurumon. One forces a Biyomon to tell him where to find the data, but before he can scan it, the inhabitants of the Village attack. They have no effect, but it allows EmperorGreymon and MagnaGarurumon to recover and counterattack. Finally, EmperorGreymon destroys and purifies the SkullSatamon brothers, but Crusadermon shows up and takes the data anyway and sends it to Lucemon while everyone escapes on EmperorGreymon and MagnaGarurumon. Though they have lost their homes, the fight restores the faith of the inhabitants of the Village of Flames in the kids and winning and increases everyone's determination to win against the Royal Knights and stop Lucemon.

The Royal Knights scan another area and are excited as there are only four areas left of the Digital World. Koji's Gotsumon friend tries to defend the statues that had released the Beast Spirit of Light from a bunch of Knightmon, but is nearly killed until the kids arrive and spirit evolve to help. While they win easily, the Royal Knights arrive and destroy the jewel that had released the Spirit, allowing them to scan the area, callously sacrificing their Knightmon to do so. They then reveal that only the Forest, Light and Ice areas are left and that they are headed to the Forest Area next before leaving. Gotsumon convinces Koji to allow him to join them in their mission to save the world and they travel to Seraphimon's Castle in the Forest Area where the Royal Knights and their Knightmon minions are unable to break in due to an energy barrier protecting the place. While MagnaGarurumon and Gotsumon take on the Knightmon, the others go after the Royal Knights who had left to try to get into the Castle from above. Attacking the barrier at its weakest point at the top, the Knights are able to start to weaken it. At the same time, someone opens a hole in the barrier for Takuya, Koichi, Zoe, J.P., Tommy, Bokomon, Neemon and Patamon and leads them to a statue of the three Celestial Digimon which contains the data for the area. Dynasmon eventually breaks through the barrier and destroys the Castle, but they are shielded by Sorecermon's spirit which had been guiding them all along. Takuya quickly evolves to EmperorGreymon to battle Dynasmon while Gotsumon and MagnaGarurumon try to destroy the Knightmon who reform no matter what they do. Crusadermon joins the fight and beats on MagnaGarurumon and Gotsumon's desire to help causes him to digivolve to his Ultimate form of Meteormon. Meteormon destroys the Knightmon and helps hold off Crusadermon. Dynasmon and EmperorGreymon fight to a draw and then fire at each other, but Dynasmon really aims for the statue and destroys it, getting the data. While EmperorGreymon and MagnaGarurumon are willing to continue the fight, Crusadermon attacks Meteormon and makes him de-digivolve to Gotsumon and the disappearing ground forces the two to choose between saving their friends or fighting. With no other choice, they save their friends, leaving only two areas left. As the gang continues on to the next area on a Trailmon, an injured Gotsumon stays behind, putting his hopes in the group saving the world.

The Royal Knights head for the Autumn Leaf Fair in the Ice Area to scan the data watched by Sepikmon through his Spirit Boomerang. Using a satellite dish created by Datamon, Takuya and Koji explain to him that there are only two areas left: the Ice Area and the Light Area where Ophanimon's Castle is. However, no one has ever been able to find the data to that area so they know the Royal Knights will head to the Fair first. At the same time, Zoe, Bokomon, Neemon and Patamon evacuate the town's residents while J.P. moves parts of the town around to break up the Fractal Code and Tommy and Koichi work with the Toucanmon (who are now fans of the gang rather than Ranamon) to build a snow catapult to be able to do something to help in the fight to come. As the Knights approach, an army of Digimon made up of Zanbamon, Gryphonmon, Pteramon, GranKuwagamon and five Airdramon arrive to try to stop them, but are easily destroyed. Takuya and Koji quickly evolve to EmperorGreymon and MagnaGarurumon to help, but only get there in time to save two Airdramon. The two battle the Royal Knights, assisted by their friends with the catapult. The others succeed in hitting Crusadermon as she battles EmperorGreymon, but Dynasmon tackles him against the town's furnace while MagnaGarurumon picks up the fight with Crusadermon. EmperorGreymon does badly against Dynasmon even with the others help until he draws on the heat of the furnace to power himself further and is able to fight back more effectively against Dynasmon. When the others attack Crusadermon, they accidentally cause her to attack them. MagnaGarurumon takes the hit and Koichi is shocked to discover he is the only one without their Fractal Code exposed. As Koichi tries to understand why he's the only one who never gets hurt, Crusadermon explains that only those with physical form display Fractal Code meaning that Koichi is only a spirit in the Digital World. Before she can explain more, MagnaGarurumon recovers and attacks her. Dynasmon's fight with EmperorGreymon exposes part of the town's data, but as it is scattered, Dynasmon is unable to easily collect it. Crusadermon holds off EmperorGreymon and MagnaGarurumon as he puts it back together, but they defeat her. Before EmperorGreymon can finish Crusadermon, Dynasmon takes his attack and puts the data back together. EmperorGreymon blows the Knights away, but they still collect the data as they go and take off to deliver it to Lucemon while EmperorGreymon and MagnaGarurumon take their friends to safety. Knowing there is only one area left of the Digital World, they fly off to the Light Area and Ophanimon's Castle to protect it.

Dynasmon and Crusadermon visit Lucemon in the Dark Area excited by the fact that they only have one area left to scan before Lucemon is free, something they promise to achieve for him. Crusadermon shows doubts about Lucemon's promise to give them the key to the human world so they can rule it, but Dynasmon chides her, saying her doubts will make her weak. The gang arrives at the Light Area and Ophanimon's Castle and decide to search for the area's data before the Royal Knights can find it, though Koichi is still troubled by what Crusadermon revealed about him being just a spirit in the Digital World. Entering the castle, the group finds Nefertimon who reveals that the castle's books hold all the knowledge of the Digital World as soon as it happens, but she is unaware of where the key to the area's data is. The group breaks up into groups to search the castle: Bokomon, Neemon and Patamon, Takuya and Zoe, Koji and Koichi and Tommy and J.P. While searching, Koichi is distracted by thoughts of how he is a spirit while Koji is excited by the idea that they can see each other all the time when everything is over, Tommy and J.P. are scared of things going wrong so J.P. does magic tricks to cheer them up and Takuya and Zoe talk about how Zoe now knows how it is to be a real friend thanks to the group. Just as she seems about to admit something to him, she finds him asleep. As the group meets up, Bokomon reveals to Koichi he knows what Crusadermon told him, but promises to keep it a secret. The next day, the Royal Knights arrive to scan the area and Takuya and Koji evolve into EmperorGreymon and MagnaGarurumon. The Royal Knights reveal they already know what the key to the area is: Nefertimon herself. When Nefertimon is unable to defeat them, she asks the two Warriors to kill her to protect the area but they refuse and attack the Royal Knights. Fighting in hand-to-hand combat, EmperorGreymon and MagnaGarurumon are able to hold their own against Dynasmon and Crusadermon, but Lucemon sends out beams of energy from the Dark Area which blast the two down and return them to Takuya and Koji. The Royal Knights destroy Nefertimon and scan the data of the area, sending it to Lucemon and finally freeing him from his prison. Lucemon travels to where everyone is and they are shocked to discover that he has the appearance and personality of a little kid. Lucemon reveals that he plans to create a new Digital World of his own and blows everyone away with a blast of energy. They are saved by an Angler Trailmon who takes them to the Yellow Moon. Despite the destruction of the Digital World, everyone is still determined to stop Lucemon and save the world.

The gang arrives on the Yellow Moon where all but Takuya and Koji despair over the fate of the Digital World and believe it is over. At the same time, Koichi is haunted by Crusadermon's revelation that he is only a spirit in the Digital World. In the remains of the Digital World, Lucemon meets with the Royal Knights and is annoyed by their demanding the key to reaching and ruling the human world and Crusadermon's lack of faith in his promise to give it to them. Lucemon orders them to travel to the moon and kill the gang. On the moon, the group finds the Dig-Eggs from the Village of Beginnings which have been relocated to the moon and play with the Digimon that have hatched from them. Two Digi-Eggs hatch and the Digimon digivolve into Lopmon and Salamon who make friends with and play with Patamon. Bokomon realizes that the two are actually the reborn Cherubimon and Ophanimon and the gang is happy because they have forgiven each other for their past transgressions and have the chance to grow up together as friends. This increases their determination to restore the Digital World. However, the babies all run away and the three Celestial Digimon reveal that the Royal Knights are on their way and the group wonders whether to run or fight. Takuya reflects back on all they have been through and decides to fight and the others agree. Takuya and Koji evolve into EmperorGreymon and MagnaGarurumon as the Royal Knights arrive and do battle with them. This time the two are more powerful than the Knights and MagnaGarurumon finally finishes Crusadermon with a point-blank attack. Enraged, Dynasmon tries to use his "Breath of Wyvern" attack to destroy EmperorGreymon, but EmperorGreymon easily destroys the attack and finishes Dynasmon with a strike from his sword. However, before EmperorGreymon can purify the Royal Knights, Lucemon appears and blasts EmperorGreymon and MagnaGarurumon away before absorbing the Knights' Fractal Code, allowing him to digivolve to his Ultimate form of Lucemon: Chaos Mode. Lucemon explains that he believes the world needs a ruler like him to keep from falling into chaos and offers the gang a chance to join his new world order or be destroyed, but they refuse. EmperorGreymon and MagnaGarurumon attack Lucemon, but have absolutely no effect on him and he retaliates, reverting EmperorGreymon into Takuya and cracking the surface of the moon. Lucemon starts to steal Takuya's Fractal Code, but MagnaGarurmon intervenes so Lucemon beats him back into Koji. However, Lucemon's attack causes the whole moon to explode.

The Yellow Moon explodes and debris from the explosion destroys the other two moons, killing all of the Digimon on them. Lucemon leaves, satisfied with what he has accomplished, not knowing that the gang has survived. Takuya and Koji are rescued by Patamon, Lopmon and Salamon who bring them back to the others who have once again lost hope. Trying to figure out how to defeat Lucemon, the Celestial Digimon reveal that the key is to combine Light and Darkness, but don't know how that is supposed to be done. Lucemon travels to the Dark Area at the core of the Digital World and uses the chaos there to start to build a portal to the human world. On a piece of one of the moons, Koji confronts Koichi about what has been bothering him and though Koichi doesn't tell him, he does ask Koji to go see their mother when everything is over. At the same time, Bokomon tells the rest of the group about how Crusadermon revealed that Koichi is only in the Digital World as a spirit and it has been haunting him and they theorize that it is because of how he came into the world: they came on Trailmon but Koichi fell down some stairs and then was suddenly there. Seeing the data streams Lucemon is sending out into space to create his portal, the group has Patamon, Lopmon and Salamon push the rock they are on towards the Dark Area and are shocked when a portal starts to form and shows Shibuya. Bokomon learns from his book that if Digimon go to the human world, they will cause utter chaos and eventually destroy it. Determined to stop Lucemon, they quickly spirit evolve to Aldamon, Beowolfmon, Kazemon, Kumamon, Beetlemon and Löwemon and attack Lucemon in the Dark Area. However, their attacks have no effect on Lucemon and after knocking Löwemon away, Lucemon blasts the others with a combination of Light and Darkness in his "Ultimate Sacrifice" attack. The kids are reverted to their human forms and Lucemon launches the same attack to finish them off, but Löwemon intercepts the Darkness, trying to use his power as the Warrior of Darkness to stop it. Löwemon fails and is consumed by the attack, killing him and reverting Koichi into a spirit. Koichi apologizes to his friends for not being able to be with them further though he has no regrets and sends the Spirits of Darkness to Koji before being scanned by Lucemon. As Koji mourns the death of his brother, the combination of his spirits and Koichi's and his and Takuya's outrage causes the two of them and the 20 Spirits of the Legendary Warriors to combine into Susanoomon who prepares to face off with Lucemon in the final battle.

Enraged by the death of Koichi, Takuya and Koji Ancient Spirit Evolve together with all the Spirits of the Ten Legendary Warriors into Susanoomon and face off against Lucemon. Lucemon offers Susanoomon the chance to join him, but knowing how evil Lucemon really is, he refuses. Lucemon attacks Susanoomon with his "Paradise Lost Punch" attack, the attack that destroyed the three moons, but Susanoomon is able to stop and injure Lucemon. However, Lucemon gets the upper hand and uses the "Ultimate Sacrifice" attack that killed Koichi on him. Reflecting on Koichi's sacrifice gives Takuya and Koji the strength they need and they split into their human selves with ten of the Spirits surrounding them, allowing them to avoid the attack. The two reform into Susanoomon and launch their "Celestial Blade" attack upon a scared Lucemon, finally destroying him. Susanoomon purifies Lucemon who reverts into two Digi-Eggs, one Light and one Dark. The Light egg explodes and tries to purify the Dark Area, but the Dark one absorbs the Dark Area and hatches into Lucemon: Shadow Lord Mode. Bokomon realizes that Susanoomon was only able to purify Lucemon's good data and his evil data was left to grow. As Shadow Lord Mode, Lucemon is now evil incarnate and unstoppable. Lucemon ignores the group and starts to head to the human world so the gang evolves to Aldamon, Beowolfmon, Kumamon, Kazemon and Beetlemon and follow him, reflecting on what they've learned on their journey and how it has made them each a better person. Lucemon arrives in the human world in the Trailmon Station and sends out a message to every electronic device in the world stating "You Must Follow Me Or Be Destroyed." Everyone catches up and attacks, but Shadow Lord Mode is too powerful and easily regenerates from their attacks. Lucemon blasts them with his "Tide of Despair" and triumphantly repeats his message to the humans.

Lucemon blasts the gang with his "Tide of Despair" attack, reverting them to human form and sending them crashing back to the ruined Trailmon Station. Takuya initially wants to continue the fight, but after Koji reminds him that Lucemon is seemingly invincible and will destroy them if they try again without a smart plan, Takuya loses hope and gives up until Agunimon, Lobomon, Kumamon, Kazemon and Beetlemon come to life to remind them that they're a team and together they can overcome anything. Grumblemon, Arbormon, Ranamon, Mercurymon and Löwemon also come to life to support them and the spirits of Ophanimon, Seraphimon and a purified Cherubimon appear to give them advice, telling them that while this will be their hardest and most important battle ever, they can beat him as a team and that Lucemon is evil incarnate in his current form and has no consciousness. Together the Spirits and human children evolve into a more powerful Susanoomon and attack Lucemon just as he reaches the surface, dragging him back to the train station. Remembering what Cherubimon had told them about Lucemon's weakness, they realize something is controlling him and spot another form, Lucemon Larva, in the orb that Lucemon: Shadow Lord Mode holds, but Lucemon Larva blasts them away before they can do anything and Lucemon launches an attack that destroys what's left of the station and starts consuming it and the little that remains of the Digital World. Following an idea by Takuya, Susanoomon flies into Lucemon's orb, absorbing attacks from Lucemon Larva all the way, and punches Lucemon Larva, knocking him out of the orb and breaking his control over Lucemon: Shadow Lord Mode. With no one in control of him, Lucemon: Shadow Lord Mode goes berserk, attacking everything in sight, but Susanoomon pins him down with his "Heaven's Thunder" attack and destroys him with "Celestial Blade," releasing all of the data Lucemon had collected from the Digital World. It seems to be over, but Lucemon Larva launches a sneak attack on Susanoomon who ejects the kids and takes the blow. Susanoomon breaks a sword out of his cannon-like weapon and splits into Agunimon, Lobomon, Löwemon. Kazemon, Kumamon, Beetlemon, Grumblemon, Arbormon, Ranamon and Mercurymon who each slice Lucemon Larva with the sword, destroying him and thus Lucemon, forever. As the Spirits congratulate and thank the kids, their D-Tectors rebuild the Digital World back to the way it was before Lucemon's reign of terror, making it an even better place now that the evil is gone. Unfortunately Lucemon's portal starts to close so the Spirits are forced to throw the kids through it before they get trapped in the Digital World. Bokomon tries to follow, but is stopped by Neemon, Patamon, Salamon and Lopmon and promises to write a book about their adventures and to never forget them. On the way home, Löwemon contacts Koji and reveals that he can sense Koichi is still alive and upon their return, which they discover to be a short time after they initially left, the gang looks for Koichi and finds him in critical condition at the hospital. However, the groups D-Tectors revive and heal Koichi before returning to being cell phones. Afterwards, the gang lives better lives using what they learned in the Digital World: Takuya spends more time with his family, Zoe, J.P. and Tommy now have real friends and Tommy is no longer bullied, Koji finally accepts his step-mother and meets his real mother with Koichi, but all promise to never forget each other and to be best friends forever.