Sei Iori aims to participate in the Gunpla Battle Championship World Tournament, but despite his skill at building models, he can't control them in battle. Then Sazaki challenges him to a Gunpla battle in order to get his hands on Sei's high-performance Gunpla. Sei accepts the battle, thinking that if he can't even beat Sazaki, then he'd be defeated instantly if he made it to the championship. But Sei is backed into a corner by Sazaki's overbearing fighting style until the appearance of Reiji, a mysterious boy who he met earlier that day. Even though Reiji has never used Gunpla before, he overwhelms Sazaki's Gunpla with his superb control technique. Sei builds, and Reiji battles. Thus the Gundam Build Fighters are born!

Having met Sei by chance, the mysterious boy Reiji insists on staying at his home and somehow even ends up coming to his school. And when Gonda, a student council executive, tries to kick out this intruder, Reiji turns the tables on him as well. Tatsuya Yuuki, the student council president and head of the model-building club, attempts to resolve the situation by saying that he invited Reiji to join the club. But Gonda, having lost face in front of the other students, challenges Reiji to a Gunpla battle purely for revenge. Using Sei's Build Strike Gundam, Reiji wins a total victory in his battle with Gonda. Then a crimson Gunpla appears before them both—the Zaku Amazing!

Sei and Reiji have now witnessed the overwhelmingly superior power of Tatsuya Yuuki's Zaku Amazing. To prepare for the day when he'll face Yuuki again in the championship, Sei secludes himself in his workshop to complete the Full Package equipment for his Build Strike. Meanwhile, Reiji goes out into the city at night and heads for a certain place—a store where men with years of Gunpla experience meet night after night to fight battles. Reiji challenges the men just for the sake of combat practice, and easily defeats his opponents. But then Ricardo Fellini, an Italian Gunpla battle fighter, appears before him! And on the day of the championship, Sei has somehow completed the Build Strike, but Reiji is nowhere to be found...

Sei and Reiji are advancing smoothly through the Gunpla Battle Championship. Then, on a certain day, a woman calling herself Mihoshi appears at the hobby shop owned by Sei's family. Sei immediately hits it off with Mihoshi, who has a wealth of Gunpla knowledge. Mihoshi makes a deep impression on Sei, and as he advances through the championship, she repeatedly comes to see him at school as well as at the store. Seeing the two of them happily discussing Gunpla, China is greatly disturbed. And Yuki, who is with her, feels an indescribable anxiety when he sees Mihoshi. On the day of the championship, Sei and Reiji are perfectly positioned to fight. But before them appears a singing woman named Kirara... Kirara, the Akihabara-style Gunpla idol!

Before the decisive battle with Tatsuya Yuki, Reiji once again goes in search of combat practice, while Sei concentrates on fine-tuning the Build Strike. China is becoming concerned that Sei is too engrossed in his work. Then, a mysterious boy named Mao Yasaka appears before the two of them. Having won the Japanese 5th Block, he has already earned a place in the World Tournament, and he says he has come to the store because he is interested in Sei, a highly skilled builder who is the same age as he is. Mao has only one goal: to determine which of them is superior as a Gunpla builder. Sei accepts his challenge, and Sei and Mao bring out their Gunpla, the Build Strike and the Gundam X Maoh. As soon as they see each other's work, Sei and Mao find themselves adrift in space...!

To have a rematch against Tatsuya Yuki, and beat him—this has been Reiji's only motivation for fighting Gunpla battles. But now that Yuki has suddenly withdrawn from the competition, Reiji has lost his purpose, and aimlessly wanders the streets. Sei, too, is frustrated that he can't have a rematch with Yuki. Seeing the two of them, China feels an indescribable uneasiness. Now that Reiji is unable to fight Yuki, where is he going to end up? But Sei vows to believe in Reiji, and looks forward to his eventual return. Meanwhile, Reiji is trembling with fear as Tatsuya Yuki appears before him. And clutched in his hand is the Zaku Amazing!

Sei and Reiji have now earned their place in the World Tournament. Together with Rinko and China, they go to the summer sea, where they can all forget the usual battles and enjoy the seaside. They head for an inn in the mountains, only to find Mao Yasaka there—he too has come to stay at the inn. What's more, it looks like he's taken an interest in Misaki, the landlady's daughter, and one way or another he keeps making passes at her. Nonetheless, Sei and the others try to enjoy their stay at the inn, but it seems that the inn is in some kind of decline. They begin to feel uneasy as more incidents occur, and then a truck crashes into the inn. From the truck emerges a man known as Blazing Tatsu, a veteran of previous World Tournaments. What could his objective be...?

Sei, Reiji, and Mao have been chosen to participate in the Gunpla Battle Championship World Tournament. Meanwhile, outside Japan, a series of qualifying tournaments have been underway in other countries to select players for the World Tournament. Among them are Ricardo Fellini of Italy, Luang Dallara of Thailand, and the Renato brothers of Argentina. Fellini's rival Greco Logan, a World Tournament veteran, is considered the favorite to represent America. But an unexpected ambush awaits him in the final round of the qualifying tournament. When the young prodigy Nils Nielsen, known as the Early Genius, reveals the hidden power of his Gunpla, the Sengoku Astray, it will shake the arena... no, the world!

Sei is working on a new Gunpla for use in the World Tournament. But, anxious about whether it's safe to keep it "as is," he has fallen into a kind of slump. When China unexpectedly ends up in a Gunpla Battle tournament limited to female players, she distracts Sei from his worries by asking him for Gunpla Battle advice. Thanks to intensive training by Sei and Reiji, China and her Gunpla, (Mr.) Beargguy III, begin piling up victories in the women-only tournament. Only one person stands in her way: Caroline Yajima, an art-contest veteran who considers herself China's rival. China finds herself in peril when she faces the Gunpla that Caroline has built.

The Gunpla Battle Championship World Tournament begins. One by one, representatives from throughout the world enter the holy ground of Shizuoka. The day before the tournament begins, Reiji skips the reception party and heads into town in search of tasty food, and there he has a fateful encounter with a mysterious girl. On the first day of the tournament, the world's top players are proclaiming themselves victorious as usual...until Aila Jyrkiäinen, who became Finland's representative by defeating the previous World Tournament winner during the qualifiers, makes her entrance and shows the world her overwhelming strength. Then Sei's and Reiji's battle begins. Their Star Build Strike, a new Gunpla created for the world championship and equipped with revolutionary new systems, finally flies into the world!

During the final battle of the World Tournament's first day, a PPSE works team entered the tournament, thanks to the sponsor's special rules. The name of its fighter is Meijin Kawaguchi, and Sei and Reiji are certain that another friendly rival has appeared. The tournament then enters its second period, a Battle Royal elimination match among all the players. An enormous diorama unfolds, and 90 Gunpla begin a fierce battle. Sei and Reiji attempt to survive the battle by teaming up with Mao and Fellini, but a huge shadow is creeping up on them...

During the second period of the World Tournament, all the players must compete in a Battle Royal elimination match. In the middle of the fighting, the battle is interrupted by the sudden appearance of a giant Mega Size Gunpla which belongs to none of the participating players. The other Gunpla have no way to deal with its overwhelming firepower, and since it isn't related to the tournament, most of the players try to avoid fighting it. But Reiji, on the other hand, boldly challenges the giant Gunpla. His seemingly reckless fighting spirit is backed up by the Star Build Strike, the new Gunpla that Sei has built. To win the fight, Sei activates the Discharge System installed in the Star Build Strike.

The World Tournament enters its third period, which consists of one-on-one battles using only the original weapons prepared by the tournament organizers. Nobody will know what the weapons are until the battle begins. Although confused by the unfamiliar weapons, the top fighters win their battles, one after another. Sei and Reiji's opponent is the Thai representative Luang Dallara, a top champion of the tournament.

The tournament has reached its seventh period, and only one period now remains. Sei and Reiji have earned a good point score, and are working their way into the top group. Then the seventh period begins, with the announcement of a Gunpla Race. This is literally a speed race, where fighters compete for position during three laps of a special course constructed inside the arena. Sei's and Reiji's Star Build Strike uses its Discharge System to make an amazing starting dash. It looks like they'll finish the race in the lead, but Baker, the secretary of PPSE's Chairman Mashita, has prepared a huge trap in the special course. The Star Build Strike is headed for danger!

Sei and Reiji have no choice but to win their next battle. But their opponent in the final period turns out to be the Italian champion Ricardo Fellini, who has been undefeated up through the seventh period. Whatever the results of this last qualifier, his qualification for the tournament finals is already decided. Now Fellini wonders whether he should give Sei and Reiji their victory, and preserve his own machine, by deliberately losing, or...? With mixed emotions, Fellini confronts the Star Build Strike.

This is a moment of relaxation, but Sei is focused on improving the Star Build Strike. When Sei refuses to let him help with the work, Reiji heads into town to prove that he too can build Gunpla. As Reiji picks through the Gunpla in a hobby store, a bearded man greets him. The man also drags in Aila, who happens to be passing by, and forcibly subjects them to a Gunpla lecture. Though his teaching methods are Spartan, the Gunpla they build following his advice is better than anyone would have expected. Reiji promptly takes his assembled Gunpla into battle, but the Gunpla that appears as his opponent looks just like a customized Gunpla that previously attacked him and Sei!

As the World Tournament finals begin, Sei and Reiji find that their opponent in the first round is Mao Yasaka. When they met in Tokyo, they swore to fight in the World Tournament, and now that promise will finally be fulfilled. But Mao senses a threat from the Star Build Strike, which was more than an even match for Fellini. With Sei's rapidly advancing building skills, and Reiji's control technique, he is likely to lose. Desperate to win, Mao goes to visit Master Chinan of the Gunpla Shingyo school of modeling arts and ask to be taught new secrets. On the day of the battle, a worn-out Mao appears before Sei and Reiji. Now begins a life-or-death battle between the Star Build Strike and the Gundam X Maoh...

The Thai champion Luang Dallara has fallen! Luang, who once fought a fierce battle with Sei and Reiji, was defeated by the Renato brothers of Argentina, dark horse contenders in the tournament. Their trick of destroying an opponent's Gunpla without using weapons, as if by magic, is a power they have kept in reserve until the tournament finals. In their second battle, these Renato brothers now face Meijin Kawaguchi. Kawaguchi presses forward with a frontal attack, but finds himself in peril thanks to the Renato brothers' clever tactics.

The next opponent for the Sei and Reiji team is Nils Nielsen, the young prodigy known as the Early Genius. His Sengoku Astray, which uses an arsenal of weapons and techniques based on Plavsky particles, is definitely a tough enemy. On the eve of the battle, Nils contacts Sei and Reiji and tells them he wants to ask them about something. If they tell him, he is willing to withdraw from the battle.

The fighting in the tournament finals is becoming ever more fierce. Having advanced to the best 8, Ricardo Fellini, the Italian Dandy, faces his next battle. His opponent is Aila Jyrkiäinen, the top fighter of Team Nemesis, who crushed the previous tournament champion Carlos Kaiser. With its speed and wealth of combat experience, Fellini's Wing Gundam Fenice puts up a hard fight against Aila's Qubeley Papillon, which has remained an undefeated legend since the qualifiers.

"We'll beat you! In our next battle, Sei and I will beat you for sure!" Aila's heart is pierced by Reiji's angry outburst, and she wonders what she is doing here. She remembers meeting Barthes, being scouted, being forced to battle, and endlessly training. Now she has no option other than fighting, even if Reiji is her opponent. Suppressing her emotions, Aila begins her confrontation with Reiji. With her Qubeley Papillon, and her own special abilities, she assaults the Star Build Strike.

As the second match of the tournament quarterfinals approaches, Meijin Kawaguchi's opponent is changed. The new fighter's name is Julian Mackenzie, and Kawaguchi and Allan are terrified to hear this name. At the Gunpla school that Allan and Tatsuya Yuki once attended, Julian was the top student, whose Gunpla building techniques and control abilities were said to be closest to those of a Meijin.

The finalists for the Gunpla Battle Championship World Tournament have been decided at last. With the finals one week away, a grand festival is held in the tournament arena. Life-sized Gundam statutes are displayed, and booths host a variety of events. For a little while, they all forget the fierce fighting of the tournament, and appreciate the fun and profundity of Gunpla with all their hearts. On the eve of the finals, Sei and Reiji have finished their preparations for the battle. Then Tatsuya Yuuki appears before them, and discards his Meijin mask.

The Gunpla Battle Championship World Tournament finals have begun at last, but the arena is shrouded in a solemn atmosphere. The Gundam Amazing Exia, the Gunpla that Meijin Kawaguchi is using against Sei's and Reiji's Star Build Strike, has been painted black. And that's not all. Like the colors of his machine, Kawaguchi's fighting style is also as grim and merciless as pitch-black darkness. Sei is bewildered—what has become of the promise he and Yuki made to make this a great battle? What has happened to Yuki? As the Star Build Strike finds itself in peril, PPSE's Chairman Mashita watches and laughs, and his gemstone gives off an ominous light.

After many ups and downs, the finals of the Gunpla Battle Championship World Tournament are over at last. However, in its aftermath, the Plavsky particle crystals have gone out of control. The particles that fill the arena are starting to materialize, as the panicking audience members rush to escape. The only way to resolve the situation is to destroy the crystals. On Nils's advice, Sei and Reiji dispatch their Gunpla, as do Mao, Fellini, China, and Aila, but they are hard-pressed by the counterattack from the crystals. Their former rivals hurry to their aid, as do the former Gunpla fighters Mr. Ral, Takeshi, and Master Chinan. Let's do it! This is Gunpla's last shooting!