The Glooms has world-changing consequences for The Heroes when the continents split apart. The continental crack-up separates The Teammates crew from The Lover Teammates Crew and the rest of the Citizen, including Kai's Ex-Wife, Angela and Older Son, Zapper. The gang are desperate to return home, but a Regular Show Villain and their ragtag crew stand in their way.
In the film's prologue, evil gloom, Hildy Gloom and Grimwold "Grim" Gloom inadvertently causes the break up of Pangaea, Kai and his Ex-wife, Angela are forced to deal with the trials and tribulations of their child teenage son Zapper"Zap", who has trouble fitting in with his peers along with his Twin brother and sister . Angela tries to support her children, but Kai becomes exceedingly over-protective. Zapper's girlfriend Mary Chumworth, the Daughter of Pythor and gwen and her twin brother Jacob tries to warn her as she tries to approach a superstar fan named Aron on whom He has a befriend. Meanwhile, Grimsborough People returns, but only long enough to drop off the elderly librarian, Constance Bell before abandoning them both. catches Zapper, clara/clary and Clark Their friend sneaking off to meet Aron, and leading to an argument and their estrangement. Shortly after, a continental break-up separates Kai from the HeroSkipper/Sins Fighters. Trapped on a moving chunk of ice with The Teammates crew and their Allies has no choice but to ride out the current. Meanwhile, a giant land shift encroaches on The Lover Teammates, Their children, and those remaining Vacation people on hotel land, causing them to make their way toward the land bridge.
Meanwhile, The Gloom, in a subplot, finds an seashell that has a treasure map on it that directs him towards an island. After violent weather pushes them further away from land, The Teammates crew's Allies is captured by a band of pirates sailing on a floating iceberg led by a Magic Baby and former Guardians of Eternal Youth, Klorgbane the Destroyer, who attempts to press them into his crew. When they refuse, Klorgbane tries to execute them, leading to their escape, which inadvertently cause the ship to sink. Buckner's first mate, a former villain and Evil spirit named Sull khan naar aka Edward along with Lilly and Lina, joins them after he is left for dead with his Wife and Sister in law.
The Heroskipper washes ashore on Switchback Cove, which Buckner's crew had earlier mentioned had a current that could let them return home. However, Edward, still loyal to Klorgbane, warns him of their presence, but is punished for not attacking the herd. Kai coordinates a plan to steal Klorgbane's new ship to return home, and enlists the aid of the hyrax inhabitants of the island. The plan works, and Lina and Lily convinces Edward to leave with them, but he stays behind to ensure Klorgbane does not catch the heroskipper. Enraged that his enemies have stolen his ship, Klorgbane quickly constructs a new ship, the Sweet Revenge, and sails after the HeroSkipper, determined to get revenge. Meanwhile, on the continent, Zapper and his friends finally begins to fit in with the Fan superstar his age, but when he tells them that he is not Fell in love with mary, the Half Human/Snakes is estranged from him. When he realizes the other super Star teens' careless disregard for danger, he turns his back on them, warning that their extinction will come sooner than they think.
After narrowly escaping a pack of sirens, Kai and Gangs return home only to find the land bridge destroyed and that Klorgbane has beaten them and taken Lover Teammates crew, Their children, and the rest of the Vacation People of HeroSkipper hostage. Mary stands up for Her love, Zapper and a battle ensues between the HeroSkipper/Sins Fighters and the pirates. Edward frees The lover Teammates crew and helps fend off his former comrades, while Constance's "imaginary" pet whale, Precious, appears and defeats the majority of Klorgbane's crew and boss. Klorgbane then attempts to kill Angela but Zapper manages to save his mother. Darlyn defeats Klorgbane in a final duel on an ice floe along with Kai and Lloyd and reunites with their family and friends. Buckner subsequently encounters a siren that appears the shape of a female Human siren, and is eaten alive while Klorgbane is Imprisoned. With Island destroyed, Kai, Darlyn and Lloyd takes their expanded family and the other people back to an island, Ninjago city. Mary is now regarded as a hero among the teenage Child, while Edward agrees to stay with Lily and Lina as a member of the HeroSkipper.
In the film's epilogue, Glooms discovers the island on the map, known as Atlantis, but their uncontrollable urge to hunt treasures in the Seashells-rich city inadvertently causes the entire island to sink when he unplugs a drain holder; Glooms are then ejected into what is now known as Death Valley, California.
In post-credit scene, Jones is eating a cupcake and cookie when Connie come to him as Jones freak out, screaming and runs to Miss bell and the Teammates crew sees Jones is chased away by Constance hitting him with pole as the Teammates crew laughing.