At night, when SpongeBob is sleeping, a small worm starts literally living in SpongeBob's head through one of SpongeBob's pores. He wakes up to feel a weird sensation, only to realize that a worm has started living inside of him. SpongeBob eventually allows the worm to stay in his head for a night, after the worm cried when tried to be forced out of him. He later named the worm Prickles, after the prickly sensation the worm has on his head.
Later, while SpongeBob continues to sleep, Prickles gives the all-clear to other worms about the good residential worm area, and they all later party inside SpongeBob's head. Gary, being completely fed up with the new worms, kicks SpongeBob out of the door as well as throwing his pants and deodorant to SpongeBob. After doing his morning routines outside his house, he goes to work at the Krusty Krab. He tells all of the worms not to appear outside during his work time or else risking losing his job.
At the Krusty Krab, Mr. Krabs notices SpongeBob with many worms peeking out of SpongeBob's pores. He warns SpongeBob against having worms on his body. However, the worms ignore Mr. Krabs' warnings and threw their trash onto the patty stove. Mr. Krabs soon had his last straw and fires SpongeBob immediately.
Walking outside, SpongeBob meets Plankton on the way. He explains to him that he got fired from having worms around him. Plankton asks SpongeBob if he could remove the worms in exchange for a deed for Plankton himself, which SpongeBob agrees to. However, when Plankton tries to get rid of all of the worms, he ends up being crippled and surrenders.
SpongeBob walks to his neighborhood and asks Patrick for help, but refuses because of SpongeBob's scary appearance. Then he asks Squidward for help, but quickly hoses on SpongeBob in attempt to get the worms out of SpongeBob.
SpongeBob, now sitting by himself, declares himself to be "SpongeBob WormPants" and laughs at the new name he has given to himself. He laughs so hard that all of the worms quickly left his head. Gary comes back to SpongeBob and he hugs Gary. Meanwhile, the worms quickly go into Squidward's house and, presumably, settle in Squidward's head.
This is the second time a short has aired after an episode. The first time was after "Help Wanted." However, "Reef Blower," which is after "Help Wanted," is an actual episode, according to production order. The short "Clam Up!" isn't an actual episode.