The first Team Arch to not have SpongeBob as the lead protagonist.
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In the medieval times, a warlord named Galton opens a portal into a parallel universe and becomes immortal, but his 4 sibling generals, Hawk, Viper, Coyote, and Rhino, are turned to stone, and the portal releases 13 immortal monsters that destroy his army and his enemies. Although he's initially proud of his immortality, Galton begins to regret his decision as time passes, considering immortality to be a curse. It's said that the portal opens every leap year, but he refuses to open it without the 13 monsters.
In the present, Team Arch is suffering from a major problem: The Digidestined have grown apart since Joe and Mimi resigned from the group to follow their own futures, and that Tai is spending more time with Team Arch rather than his respective group; so, Sandy and Chad Perkins have Tai sent to El Salvador for "leader training", where he protects a village from Honduran bandits, earning the nickname "El Tocayo". Izzy works as an IT specialist at Vanguard Inc, occasionally with Davis, who also works as a part-time birthday party entertainer called "Allstar Alan", while Sora, Matt, TK, Kari, and Ken continue to fight crime alongside Team Arch, with TK giving his role as second-in-command to Sora. However, they have competition as a conceited vigilante known as "Dark Prince" tends to show off his crime-fighting tactics.
One day, Fujitaka, Sakura, SpongeBob, Yugi, and Nate travel to El Salvador to acquire a statue and find Tai, telling him that the Digidestined have drifted apart. While SpongeBob stays with Tai, the others return to San Francisco with a statue for wealthy tycoon Malcolm Heller. After fixing an accident at Heller Tower, they deliver the statue, who turns out to be General Hawk. After they leave, Heller hires the House of Radcliffe to search the city for the 13 monsters before the portal opens again. The following night, Sora's team encounters Matt's new band, Knife Of Day (Akira Takahashi, Koji Nakajima, Hiroshi Hashimoto, and Yutaka "Yuta" Kobayashi), who tend to do a little vigilante work themselves and join them in hunting criminals. Heller, who is actually Galton, reanimates his four stone generals using technology created by his company.
Around the same time, Tai and SpongeBob also return to the lair in Japantown, reuniting with the Digidestined and the rest of Team Arch. Perkins forbids the Digidestined from fighting until they can act as a team again. While training, SpongeBob and the Digidestined encounter one of the 13 beasts, a hulking gorilla-like monster with horns and teeth, battling the House. Matt and Davis engage the monster, going against Tai and Perkins' orders. During the fight, the four stone generals easily defeat and capture the monster, while the heroes escape when the police arrive. The House returns to confront Heller and the generals about the monsters, but Heller assures them not to worry.
The next morning, having learned of what happened last night, Perkins scolds the Digidestined for their disobedience, but doesn't punish them when SpongeBob explains about the monster, and suggests that they investigate. Perkins allows them, but says that he'll give out the command to engage.
While the heroes investigate, the generals and the House continue to capture 9 of the monsters. When Davis and Ken visit KOD, they encounter Scrimjeer, one of the monsters, and witness its capture by the House and the generals, who spot them after Koji accidentally knocks some stones over. Despite a successful escape, Ken is knocked unconscious by a tranquilizing dart. Davis and KOD take Ken back to the apartment and alert the others for help. After examining Ken's condition, they examine the dart and a throwing star that was also recovered, and reveal the identities of Galton and his generals, who turn out to be Heller and the statues that Fujitaka had been collecting for him. As Ken revives, Matt suggests they pursue Galton, but Tai forbids him to go until Perkins gives them his permission, leading to an argument that results in Matt angrily quitting the team and leaving. KOD tries to follow Matt, only to encounter Dark Prince, who reveals his identity to them.
With Matt out of the team, the rest of Team Arch plan their next move, while Izzy discovers the next portal will open over Heller Tower. Perkins tells Tai that his team is still incomplete, and that he knows what he must do. After 11 monsters have been captured, General Hawk questions Galton's plans for them and the portal. The generals conspire to betray Galton, wanting to continue their quest to conquer the planet by remaining immortal and ruling the planet with an army of monsters from the portal. Meanwhile, Dark Prince and KOD encounter the Jersey Devil, one of the remaining monsters, at a diner, and after a comical fight, they drive it off. Tai, Sora, TK, Kari, and Izzy encounter KOD and Dark Prince, believing him to be nothing but an arrogant thug, despite their appreciation of his crimefighting intentions. After a lengthy chase and a fight, resulting in Dark Prince's helmet getting knocked off, they discover that Dark Prince is actually Matt, who had been secretly going behind Sora's back to fight crime alone. Sora and Matt argue about his double life and how much things have changed since Tai left. Matt wants Tai and Sora to fight him, but TK decides to get involved and another fight breaks out between the two brothers, resulting in Matt injuring TK, and running away in a fit of guilt and shame. While Tai, Kari, Sora, Izzy, and KOD go after Matt, the House and the generals seize a weakened TK, intending to substitute him for the 13th missing beast. The others try to save TK, but the House and the generals leave with him.
Matt, now revealing what happened, decides to make amends by rescuing TK, with Perkins finally deciding that the time for hiding is over. While the heroes prepare to invade Heller Tower, the portal opens, but Galton discovers TK and his generals' treachery. Meanwhile, Team Arch fights their way through the House and breach the tower. After rescuing TK, Team Arch encounters Galton, who reveals the truth: He only wants to send the monsters back to where they came from and be freed from his curse of immortality. With the truth revealed, Team Arch decides to help him, but the generals appear and reveal their plan to conquer the world.
The generals attempt to persuade the House to join them, but Nolan refuses and tells the House, except his top cronies, to head back home, and work with Team Arch to search for the final monster. While the Star Alliance, Yugi's group, Nate's group, and the House search for the monster, SpongeBob's group and the Digidestined fight the generals, while Kaz's group, Hanayo's group, Gingka's group, Team Core-Tech, and Galton fight off numerous monsters emerging from the portal. The search team arrives at the tower with the last monster, who crashes into the generals, dragging them into the portal before it closes. Nolan warns them to enjoy their victory while it lasts, cryptically claiming they will soon contend with faces from their past before vanishing. Galton, now mortal, honors Team Arch, thanking them for fulfilling his wish and hands them his helmet before dissipating.
The movie ends with Perkins placing Galton's helmet among his personal trophy collection, while Team Arch, with a fully restored Digidestined, now rebranded as the Digital Heroes, train in the streets of San Francisco.
