WARNING: I killed off another character.
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Intro Song:
In the opening credits scene, Emma gives SpongeBob a special performance as a thank you gift for leading the team through so many adventures. However, after her performance, she begins to think about their past missions, realizing that she's the only one of Team Niji to hardly do anything.
Meanwhile, fed up with having to wait around for Slinger and his gang to attack, Kaz decides to lead JET into a premeditated attack on Slinger's compound, which had been recently located in the wilderness. Despite Team Arch warning them to stay put, Kaz blatantly defies orders and goes off with the rest of JET in tow on the way to the compound.
At the compound, Slinger and his gang prepare to launch an attack of their own. However, it nearly gets scrapped, when Shizuku begins to look back on the many escapades between Team Arch and Slinger's gang. She was about to talk to Slinger about their old invasion on Sacramento, when the Chip & Fish Quartet (Charlton Farrow, Herbert Ingram, Irvin Snyder, and Paxton Hurston) appear in their compound, proposing that they should work together to take down a common enemy: Team Arch. Slinger and his gang wholeheartedly agree, but Shizuku is still skeptical.
Back in Sacramento, SpongeBob gathers the team to start a rescue mission to retrieve Kaz and JET. As they prepare, Ayumu, still worried about Shizuku, begins to wonder about the CBI having Shizuku on their Most Wanted Board, despite the fact that Shizuku isn't really evil. Just before the team leaves, Ayumu decides to stay behind to confront the CBI's higher-ups.
Meanwhile, JET invades Slinger's compound, taking out most of his soldiers, before ending up at the main control room. There, JET handles the girls of Slinger's main 9, except for a quietly defiant Shizuku. Although they secure a victory, JET is swiftly thwarted by C&F and taken hostage, except for Sanya, who escapes to search for SpongeBob.
At CBI's head office, Ayumu confronts the Director about Shizuku on the Most Wanted, demanding for them to remove her, but the Director cuts a little deal with Ayumu, suggesting that she try one more time to bring Shizuku back to her senses. In return, the CBI will pardon Shizuku.
During the journey, SpongeBob becomes worried about how Team Arch's recent missions have been getting more and more dangerous, but the rest of the team assure about how they've always been together in such dangerous adventures. Suddenly, Sanya appears and warns them about JET's capture.
Back at the compound, Kaz blames himself for getting JET into their current mess, but Fiona comforts him, claiming that people can sometimes be desperate to do the right thing. They are suddenly interrupted by two escaping prisoners, who break them out and bring them along. They introduce themselves as Kanon Shibuya and Chisato Arashi, two school idols who were on a mission to rescue fellow group member, Keke Tang, from a plan conducted by C&F.
At the compound's entrance, Team Arch arrives, only to discover Slinger's gang and C&F escaping in an airship belonging to the latter with what appears to be an advanced cannon, prompting the team to follow them, which unfortunately results in JET, Kanon, and Chisato missing them.
Up in the sky, Team Arch chases Slinger's gang and C&F in a climactic pursuit, but the latter alliance lose the former team by causing them to crash into a forest below them. As they celebrate, Shizuku eavesdrops on a private meeting between C&F, learning that they will use the cannon to unleash a deadly virus, made from Keke's blood, on Sacramento, and betray Slinger's gang by casting them off as scapegoats, leading to the four of them pretending to be heroes. Disgusted, Shizuku goes back to Slinger to warn him.