After Flint Lockwood and his friends save the world from the food storm in the first film, super-inventor Chester V, the CEO of Live Corp and Flint’s childhood idol, is tasked to clean the island. He relocates Flint, his friends, and the citizens of Swallow Falls to San Franjose, California. Unbeknownst to Flint, the FLDSMDFR survived the explosion and landed in the center of the island, and Chester is determined to find it. Chester invites Flint to work at Live Corp, where he meets Chester’s assistant Barb, a talking orangutan with human intelligence. Six months later, Flint humiliates himself during a promotion ceremony when his invention, the ”Celebrationator”, explodes. Meanwhile, Chester is informed that his search-parties on the island have been attacked by monstrous cheeseburgers named cheespiders (a combination of a cheeseburger and a spider) which are trying to learn how to swim. Seemingly fearing the world’s inevitable doom, Chester tasks Flint to find the FLDSMDFR and destroy it once and for all. Despite Chester’s demands to keep the mission classified, Flint recruits his girlfriend, meteorologist Sam Sparks; her cameraman Manny; police officer Earl Devereaux; Steve, a monkey who communicates via a device on his chest; and ”Chicken” Brent. Much to Flint’s dismay, his father Tim joins the crew and they travel to Swallow Falls on his fishing boat.
Upon arriving back at Swallow Falls, they notice that a jungle-like environment made of food has overgrown the island. Tim stays behind while Flint and the others investigate, finding a vast habitat of living food animals called foodimals and meet a cute strawberry nicknamed Barry. Tim, searching for sardines at his abandoned tackle shop, encounters a family of humanoid pickles and bonds with them by fishing. Chester discovers that Flint allowed his friends to join him on the mission, so he travels to the island with Barb, chagrined and determined to separate them, and he arrives just in time to save them from a Cheespider. Flint then finds his old lab and invents a device to find the FLDSMDFR. After escaping a Tacodile attack, Sam notices that the foodimal was protecting its family, and begins to suspect Chester is up to no good. Sam attempts to convince Flint to spare the foodimals, but Flint is intent on impressing Chester. Sam leaves in anger, and Flint’s other companions go with her. In the jungle, Manny confirms Sam’s suspicions when he reverses the Live Corp logo to reveal the ”Live” as ”Evil” spelled backwards. In addition, Sam proves that the foodimals mean no harm by taming a Cheespider. They also learn that the foodimals had known the truth about Live Corp before. Upon realizing Chester’s intentions, the group is then ambushed by Evil Corp employees.
Flint finds the FLDSMDFR, but notices a family of cute, friendly marshmallows and becomes hesitant to destroy the machine. Chester immediately seizes control of the FLDSMDFR and announces his plot to make his updated line of food bars out of the foodimals. A crushed Flint is knocked into the river but rescued by the marshmallows. Flint is taken to his father, and they and the foodimals all work together to allow Flint and Barry to infiltrate the Evil Corp building that is under construction on the island. Barry frees the trapped foodimals while Flint confronts Chester, who threatens to make food bars out of his friends. Chester makes numerous holograms of himself to overwhelm Flint, but Flint uses the Celebrationator to expose the real Chester, allowing Flint to rescue his friends. An army of foodimals led by Barry arrive and fight Chester’s employees. Chester tries to make off with the FLDSMDFR, but is thwarted by Barb, who has a change of heart and Chester gets eaten by a Cheespider. With the island safe from Chester V and Evil Corp destroyed, Flint returns the FLDSMDFR to its place and frees it from Chester’s control and the foodimals continue to live in peace as more are born. The film ends with Flint fishing with his father for the first time, finding it enjoyable. In the mid-credits scene, Barb was trying to asking out Steve and he was trying to eat a banana sandwich.