While foraging for food in the forest, Saboteur Toru Acura encounters Chaika Trabant, a white haired wizard with a white headband who carries a coffin. A man eating unicorn chases after Chaika which Toru hold off the beast using his Iron-Blood Transformation before Chaika kills it using her magic Gundo sniper rifle. As gratitude, Chaika buys Toru lunch only to be mistaken by his sister Akari Acura of slacking off. Meanwhile, Alberic Gillette and his men from the Gillette Corps meets with Roberto Abarth, a war hero who fought against the Gaz Empire five years ago and asks Abarth an item he acquired from the war but is told to leave. Elsewhere, Chaika hires the Acura siblings to steal an item in Abarth's mansion. As Toru, Akari and Chaika sneaks into Abarth's mansion that night, they are caught by Abarth himself who mistakes them for thieves hired by Alberic to steal his item. As he's about to use his magic to eliminate them, Abarth is shocked when he recognizes Chaika.

Abarth is shocked to see Chaika as he believed she died. After escaping him, Chaika explains Abarth's mansion is his Gundo which allows him manipulate the mansion and the only way to stop it is to destroy it's magic source. As Chaika and Akari searches for the source, Toru distract Abarth by fighting him. Eventually they finds the magical source, a severed left hand in a glass jar, the item Chaika is looking for, allowing Toru to defeat Abarth. As they leave the mansion, the trio are attacked by the Gillette Corps who demand they hand over Chaika and the magical hand. Akari drags Chaika to safety while Toru, carrying the glass jar, sends the Corps into a chase around the city before fighting one of their members, Nikolay Autotor. Toru is soon corned by Alberic, Viivi Holopainen and the Corps magic vehicle. Alberic reveals to him that Chaika is actually Chaika Gaz, the daughter of the dreaded Emperor Arthur Gaz of the Gaz Empire, who died at the end of the war after he was killed by the Eight Heroes, who later took parts of Arthur's body. Alberic and his organization fear if the world knew Chaika is still alive, the Gaz Empire would be reborn by Gaz loyalists and his remains are dangerous magic sources, which would reignite the war. Despite this, Toru is unfazed as he enjoys the prospect of war returning before escaping. Chaika reveals to Toru and Akari that she is gathering her father's remains so he can be given a proper burial. Toru and Akari decides to help Chaika in her quest which she is thankful.

With Chaika's coffin giving them attention, Toru has wrapped in cloth while they search for another of the Eight Heroes who has a part of Arthur's remains in the town of Ipsom. Meanwhile, the Gillette Corps receives word from their superiors, the post war Kleeman Agency, are unable to send reinforcements. As they have lunch, the trio learns the ruler of Ipsom, Dominica Škoda, a dragoon cavalier and one of the Eight Heroes, lives nearby a dangerous forest. The trio is almost caught when they learn the Gillette Corps are in town but thanks to the help of Guy, a young man who appears as a hologram and Chaika's informant over her father's remains, he leads them to a lake where they use an abandon magical vehicle as transport and where Dominica's home is. As Chaika fixes the vehicle, the Gillette Corps looks over past information on how they caught fakes who pretended to be Chaika and wonder if Chaika ever existed. On their way to Dominica's home, Chaika reveals she was out of the country when her father was killed and doesn't have memories during the war. The trio is soon attacked by Orthrus but are saved by a female knight.

The female knight introduces herself as Dominica Škoda and allows the trio to stay in her mansion. Toru suggest they ask Dominica to hand over Arthur's remains to them peacefully before using force if that fails which Chaika is conflicted since Dominica saved their lives and is kind to them. The next day, Toru asks Dominica for Arthur's remains which she will give them if they can defeat her in a match tonight. As they prepare themselves, the group realizes something strange about Dominica as she doesn't recognize Chaika despite being one of the Eight Heroes. During their match, Toru and Akari fights Dominica in their Iron-Blood Transformation forms but her Dragoon magic powers proves too much for them. However, Toru manages to figure out that the Dominica they are fighting is not her but her Dragon taking her master's form which the dragon reveals its true form. Using their skills, Toru, Akari and Chaika defeats the Dragon. The Dragon reveals Dominica passed away after the war but due to their close bond, she was unable to forget her master hence she took her master's form. As promised, the dragon, Fredrika, gives them Arthur's eyes and decides to follow Toru, Akari and Chaika in their journey by transforming into a young girl.

Heading to the town of Perimeral, Toru, Akari and Chaika are ambushed by a red armored sword fighter and her two companions. Toru captures the warrior but is shock to discover that she looks like Chaika but with short hair and a red headband. Chaika is captured by Red Chaika's companions but both groups are forced to flee after the Gillette Corps arrives. After bribing her with food, Red Chaika reveals her name is Chaika Bohdan, who also claims she's Emperor Arthur's daughter and wants to gather her father's remains but unlike their Chaika, Red Chaika wants to use the power of father's remains to take revenge against the Eight Heroes and the subjects who abandoned her father during the war. Meanwhile, Red Chaika's companions reveal to Chaika that there are other girls named Chaika who are also clamming to be Emperor Arthur's daughter. Elsewhere, wizard Mattheus Callaway and Catboy Leonardo Stola split up with the Gillette Corps to track Toru and Akari but instead find Red Chaika's companions. Eventually, a deal is reach where both groups head to a waterfall to exchange their Chaikas which both Chaikas meet each other face to face.

Cockatrices controlled by Mattheus attack the meeting place, forcing David and Selma Kenworth to escape with Chaika while Toru, Akari and Red Chaika fight them. Returning to their vehicle with Red Chaika where Fredrika is waiting for them, Toru and Akari plann their next meeting. Meanwhile, the Gillette Corps are ordered by the Council of Six Nations to deal with farm riots much to Gillette's frustration as the Council believe Chaika is nothing but a myth. As Toru and Fredrika waits for Akari to return to find out where the next exchange point will take place, Red Chaika asks why Toru is helping the White Chaika and offers him to join her instead as she can bring back the war. Both groups meet at Perimeral where they exchange hostages and despite Red Chaika's offer, Toru remains loyal to his Chaika. As they leave town, Chaika wonders if she really is Chaika Gaz but Toru doesn't care as what matters is that she's real. Toru group is stopped by Red Chaika and David who suggests they should join forces so they can find Arthur's remains quicker. But when Red Chaika reveals there can only be one Chaika Gaz, Toru and Akari fights her group, forcing them to flee. Toru fears not only will they face the Gillette Corps but the other Chaikas as well.

Guy informs Toru and his group that the next Hero they can find, Simon Scania, was last seen at The Valley of No Return four years ago. However, they are ambushed by the Gillette Corps before escaping using Fredrika's Dragon form. Arriving at the valley, they noticed a fog made by magic in the valley before Toru, Akari, Chaika and Fredrika accidentally falling in. In the fogged valley, Akari, Chaika and Fredrika, in a protective barrier, notices the fog causes illusions which Toru believes he and Chaika survive the fall and became a couple only for Gillette to take her away. The trio manages to drag Toru into the barrier, where they decide to destroy the machine that makes the magic fog. Using Chaika's magic to temporarily dispel the fog, the group manages to find and destroy the machine. With the fog cleared, the group finds Simon, now mad and delusional. Simon reveals he created the fog machine in revenge when his wife and his best friend betrayed him in order to show anyone going into the fog the pain of being betrayed by a loved one. After getting Arthur's leg from the machine, the group leaves Simon behind while the girls question Toru on his illusion.

The head of the Kleeman Agency, Konrad Steinmeitz, ask Alberic to take a break on searching Chaika Trabant. While he does some research on Emperor Arthur, he reveals to Vivi and Zuita Brusasco that he could not find information about the man before the war, which raises his doubts. Elsewhere, Toru and his companions encounter a group who calls themselves the "Neo Gaz Empire', who aims to bring back the Gaz Empire under a blonde haired girl who calls herself "Princess Chaika". While Chaika befriends the princess, Toru, Akari and Fredrika have suspicions about the group. Their suspicions are confirmed after defeating the Neo Gaz's men, the group admits they are actually former Gaz Empire citizens who turn to thievery after being abandoned by the Six Nations. While Toru wants to leave, Chaika begs him to save the fake Princess Chaika, whose real name is Julia, after learning she got captured in a failed breaking and entering. Toru and comrades rescues Julia, which she and her friends thanked them but not before Toru learns, even during his rule, many of his citizens don't know much about Emperor Arthur. Meanwhile, the Council of Six Nations deals with a rebellion by Duke Gillard Gavarni who controls a floating fortress.

Running low on magic fuel for their magic vehicle, Toru's group is unable to find any shops still selling them due to the people celebrating the Anniversary of the End of the War against the Gaz Empire. Despite Chaika offering to use her memories as a substitute magic fuel, Toru refuses after learning Chaika loses her memories after using them. Meanwhile, the Gillette Corps celebrate the Anniversary in their own way before being summoned for an emergency mission. While Toru's group searches for any shop still selling magic fuel, Toru tells Chaika about his childhood. Toru reveals he and Akari grew up in village called Acura where the people trained to become Saboteurs. Despite his eagerness to join the Gaz Empire War, his mentor Shin tells Toru he is reckless. Toru also looked up to Jasmine, a woman who was part of a convoy of traveling merchants who traded with the Acura villagers, who Toru saw as a big sister figure. However, one night, the convoy was attacked by bandits who killed the merchants. Despite his efforts, Toru was only able to find a dying Jasmine, who comforted the boy in her last moments. Even though the villagers were able to kill the bandits responsible, Jasmine's death left a deep impact on Toru, which shaped him to be the man he is now and tells Chaika to never forget her memories, both good and bad. After finally finding a shop that still sells magic fuel, Toru and Chaika learns from the shopkeeper that Duke Gavarni of Iveco has acquired one of Arthur's remains from one of the Eight Heroes and decides to go there.

Arriving at Iveco, Toru realize something strange when he and Chaika notice there are no young girls and a lack of magic fuel. They soon learn from a shopkeeper that Duke Gavarni has been using all of the town's magic fuel to power the floating fortress Soara and his soldiers are kidnapping the town's girls and bringing them to his fortress where they are never seen again. Toru's group sneaks into Soara by having Akari disguise herself as one of the many girls being taken by the Duke's men where she helps Toru, Chaika and Fredrika get in by the fortress windows, unaware that Vivi and Zuita have sneaked in as well. Meanwhile, the Council decides to take action against Duke Gavarni by launching their own floating fortress Stratus. Konrad warns Alberic to get Vivi and Zuita out before the Council forces will destroy the Soara. Toru's group tries to find the Soara's magic engine only to be ambushed by the Duke's soldiers where Toru and Chaika escapes, Fredrika speared and thrown from the floor and Akari captured. Akari is brought to Ricardo, the Duke's youngest son, who reveals the Duke and his family were killed by Ricardo himself and he, his wizard adviser Grad Lancia, and another accomplice have using the Duke's name for their own plans before Grad uses a mind control spell on Akari. Toru and Chaika encounters a girl named Layla whose asks for their help in rescuing the women captured by the Duke's men but is led into a trap when Layla is revealed to be Ricardo and Grad's accomplice who kidnaps Chaika while Toru faces off a mind controlled Akari.

Toru is rescued by Vivi and Zuita where the three of them agree to an alliance to try and escape the Soara before the Stratus and the Council's forces destroy it. Elsewhere, Chaika is brought into a room by Layla where the latter reveals she knows who Chaika identity is. Meanwhile, Toru, Vivi and Zuita learns the horrible truth on what happen to the girls captured by the Duke's men; the girls are tortured by Ricardo which Grad and Layla uses their painful memories as magic fuel for the Soara. Layla reveals herself to Chaika Trabant that she too is a Chaika (Blue Chaika) and reveals the terrible truth; neither she or the others who look like her are the real Chaika Gaz. Layla reveals the Chaikas were created by a mysterious group who gave them different skills and personalities to help them gather Arthur's remains by making them believe they were Arthur's daughter which Layla herself learned from a mysterious creature and remembering Princess Chaika was killed by the Eight Heroes. Chaika goes into denial but Layla tells her to accept the truth while she goes to take her revenge against the group that used her by restarting a war. Fredrika arrives to rescue Chaika only to be killed and dragged by one of Grad's spider monsters. Elsewhere, Alberic and Leonardo tries to convince the captain of the Council Forces to stand down so that his comrades can escape but when he refuses, Alberic resorts to threatening the man's life. Corned by a mind controlled Akari and the Duke's men, Vivi and Zuita hold them off while Toru tries to rescue Chaika.

Despite Alberic's attempts, the commander of the Stratus is unfazed and orders the Stratus to fire their magic cannons on the Soara. As the Soara and Stratus fire each other, Zuita is able to free Akari from Grad's mind control while the latter explains to Zuita and Vivi what happened since she was captured. Despite the revelations of her true origins, Chaika is detmerine to continue her quest to gather's Arthur's remains while Toru fights to reach Chaika. Akari, Vivi and Zuita discovers Fredrika is still alive, having created a second body and leads them to Chaika's last known location only to encounter more of Grad's spider monsters. The Soara fires one of their magic cannons on the council forces with Alberic caught in the blast which Leonardo only finds Alberic's sword. As the Soara heads to Cadwell to destroy capital of the Wiemac kingdom, the heavily damaged Stratus launches a suicide attack, sending the Soara sinking to a lake. An injured Toru rescues Chaika from Ricardo by stabbing the boy while Akari kills Grad, ending his control of his minions. After retrieving Arthur's left leg, Toru is shoot by Layla's crossbow bolt who attempts to kill Chaika, angered that Chaika still continues her quest despite learning the truth. However, Layla is distracted when she sees Guy, allowing to Chaika to shoot her with her Gundo sniper rifle. Chaika rescues Toru from drowning and with help of Fredrika's Dragoon form, she, Toru, Akari, Vivi and Zuita escapes the Soara before it sinks to the bottom. Layla decides to stay with a dying Ricardo so they can be together. When Vivi and Zuita returns to their group and learns of Alberic's death, Vivi screams in grief as her hair and eyes turn white and purple respectively. After Chaika reveals to Toru, Akari and Fredrika her true origins from Layla, Chaika still wants to continue her quest which they all agree to help her as they drive off to their next destination.