The peaceful Neotopia is one day attacked by the invasion forces of the Dark Axis. Shute, a clever, inventive boy stumbles upon the villains, a mysterious robot named Captain Gundam, and the adventure of a lifetime!
Captain Gundam is unable to activate his 'Soul Drive', even though it activated once before. Eventually Captain realizes that Shute has an effect on it. Meanwhile, Zapper Zaku has new orders from his immediate superior, the commander. Find Captain Gundam and wipe him out!
After two defeats, the Dark Axis commander assigns another officer to Zapper Zaku's platoon, Grappler Gouf. Even with Shute's help, Captain is nearly overpowered by the two villains. That is when a new gundam appears to even the odds!
Zero's appearance does little to calm the commander. While Captain was viewed as a minor annoyance, he and Zero together could be a threat. So he has Zapper Zaku and Grappler Gouf bring the gundams to the Dark Axis base. It's up to Shute to rescue the gundams!
After successfully saving Captain and Zero, Chief Haro, leader of the S.D.G.(Super Dimensional Guard) makes Shute an official member of the Superior Defender Gundam Force. Good thing, too, because the Dark Axis commander has added the weapons-loving Destroyer Dom to the Neotopia invasion force!
With the Dimensional Transport Device ruined, Bakunetsumaru is stuck in Neotopia. However, the quick-tempered Musha Gundam won't join the Gundam Force. he might want to change his mind, because Zapper Zaku has taken control of a giant robot statue, and is going on a rampage through Neotopia Peace Park!
Captain's instructor, in the form of Gunbike, has come to train the Gundam Force. They'll need all the training they can get, as Grappler Gouf has hijacked a trainline!
Zero is being haunted by the memories of his failure to protect the kingdom and princess of Lacroa. Meanwhile, Destroyer Dom and two Zakos wreak havoc at a facility where Sayla is making a giant birthday cake for Mayor Gathermoon!
Bakunetsumaru and Dr. Bell Wood are in a fierce argument. Bakunetsumaru needs the Dimensional Transport Device repaired, in order to return to Ark, but Bell Wood feels fed up with the project. Meanwhile, four Zakos take control of a massive digging robot, and use it to wreak sub-terrenian havoc!
Shute is writing an essay about "friendship", and each member of the SDGF has their own definition for it. Meanwhile, after some prodding(I.E., blasting) from the commander, the Dark Axis trio cooks up a triple attack to use against the Gundams.
A slip-up with Bell Wood's Dimensional Transport Device sends the Gundam Force to the ruined kingdom of Lacroa, Zero's homeland. there, they meet three triplets who survived the Dark Axis invasion, and Talgeese, Knight of the Tempest, a warrior who joined the Dark Axis!
Trapped in the Dark Hole of Lacroa, the Gundam Force are separated. While Captain deals with Bakunetsumaru's fear of ghosts, Shute and Zero have to handle three spunky triplets, who don't think Zero can save Lacroa. What's more, the triplets are guarding the Spirit Egg, something Talgeese needs if he's to unlock the powers of Lacroa's Spirit Tree...
After escaping from the Dark Hole, the Gundam Force are reunited. But they're not done yet, as they have to fight Talgeese in order to protect the Spirit Egg!
Two Zakos disguise themselves as mobile reporters and interview the Gundam Force, trying to learn their secrets. The GF sees through the ruse, but play along anyway, and they gain more then they lose. Afterwards, the Spirit Egg hatches into a cute, fuzzy blue creature...that breathes fire!
The Komusai II, an improved version of the Komusai, goes haywire because two Zakos dropped controll horns on it. An sense none of the core members of the Gundam Force are fast enough to catch it, it's time for a new Gundam, GunEagle, to fly!
During the last battle, the Komusai II was knocked into the ocean. Captain, Shute, and the new GunDivers submerge to find it, and learn the secrets of the Dark Axis from it. Speaking of the Dark Axis, they're also underwater, looking for the Komusai II as well!
Fed up with the failures of his usual lackies, the commander calls in two renegade Musha Gundams from Ark. One Musha, Ashuramaru, has a bone to pick with Bakunetsumaru, and won't rest until the score is settled!
After the run-in with Ashuramaru, both Captain and Bakunetsumaru are taken to Blanc Base for repairs. Then, Zakorello gates start appearing all on the sensors, calling the Gundam Force away from the base! But it's no invasion, it's a trick! Corbamaru, another renegade Musha gundam, plans on adding Blanc Base to his record of conquered castles, and Shute, the only one who stuck around, can stop him from send Blanc Base crashing into the ground!
The time has come for the long-awaited duel between Bakunetsumaru and Ashuramaru! And, to really make things interesting, a new Musha gundam appears! The Daishogun of Perfect Virtue, a mysterious being who can twist reality, creates an ample stage for two warriors. Both sides watch on as the Musha gundams battle each other in a fight...to the finish!
The Daishogun of Perfect Virtue is staying at Shute's house, and everyone not in the S.D.G. thinks that sense he is a friend of Bakunetsumaru, the Daishogun is a movie star. With everyone focused on the Musha Gundams, Zero and Fenn are shoved out of the spotlight. Speaking of Lacroa, a Pawn Leo appears, looking for the Spirit Egg.
Talgeese is back, and with two new warriors, attacks the Gundam Force in Neotopia! As the SDGF fights against the three evil knights, Fenn must awaken as the Feather Dragon of Lacroa's legend.
It's another peaceful day in Neotopia, and the Gundam Force are starring in a movie. But the overacting is cut short when the Dark Axis attacks Blanc Base with the Big Zam, a virtually unstoppable super-tank!
With Blanc Base down, the Dark Axis start phase two of their invasion. Their Doga bombers attach control horns to the mobile citizens, and it won't be long before they have complete control over the robots in Neotopia! To stop this, the S.D.G. initiate the 'Captain System', but to do that, they need the Re-equipt Ring, which has fallen behind enemy lines...
While in 'Brain World' Captain discovers a link to the Dark Axis' Bagu Bagu. But while he investigates, Zako Red steals the Soul Drive! With their invasion complete, the Dark Axis commander makes himself known. Commander Sazabi gives Neotopia an ultimatum: Surrender or be destroyed!
With Captain out of action, and the other Gundams out-gunned, it falls to Shute to take the Soul Drive back. Can he do it?
With his Soul Drive back in place, and the petrification effect of the Bagu Bagu reversed, Captain Gundam faces Commander Sazabi in a battle to decide the fate of Neotopia!