The film starts out with Godzilla battling Mechagodzilla then fallling into the water which he knows is where Spongebob Squarepants lives. He goes and finds Spongebob and then rips the roof off of his house and then Spongebob runs for his life. Gary ducks as Godzilla swings his tail over Spongebob's house and then destroying it. Spongebob runs for squidward as he is playing his clarinet. Squidward looks out his window and sees Godzilla's headed for his house and then jumps out the window and then running to the Krusty Krab. He alerts Mr. Krabs and tells him that Godzilla is headed for the Krusty Krab but he ignores him and tells him to get to work. Spongebob gets Patrick and then Patrick insists that they destroy the monster and then destroy Bikini Bottom for good so he dosen't come back again. Spongebob comes up with a plan to kill it without harming Bikini Bottom. So they went and got the army and told them they needed to destroy Godzilla before he kills all of Bikini Bottom. Meanwhile, Mr. Krabs is out with Squidward when Godzilla approaches and then everyone jumps out the windows and then Squidward says that everybody is weird these days. After Mr. Krabs finishes his explanation, Godzilla breathes his atomic breath at the Krusty Krab and that kills Squidward and Mr. Krabs. While Patrick insists that Spongebob kill the monster, his mind goes blank. Spongebob wakes up Patrick so they don't die. Godzilla runs toward Bikini Bottom and destroyes the town in only a few minutes. Later, Swift fishman and Patty Girlfish team up with Spongebob and Patrick to kill Godzilla. Godzilla later is surprised when he sees a heat blast that will incenirate the entire world and then they run for their lives but it cathches up with them and then the film ends.