After causing chaos at a beauty salon, Lilo and Stitch meet the hair-eating experiment that made Jumba nearly bald. They called the experiment "Clip". However, the hairball gets lose and threatens to eat up all the hair on the island.
Lilo and Stitch have captured a new experiment, he is insanely cute too, and charms all of Lilo's friends, all but Stitch. There's one other problem too, he's a ticking stink bomb.
Lilo goes to an Elizabethan Fair with the hula girls, but Stitch can't join her as no dogs are allowed and Mertle refuses to be with Lilo. Stitch and Mertle then team up to fight against a metal-eating experiment.
While at the post office mailing a letter to her pen-pal, Lilo finds experiment 509 pod. Jumba reveals it is an extraterritorial weed that grows out of control, bent on destruction. He deems too dangerous and locks away in a draw. Later, Lilo bets Myrtle that she can win the orchid competition. No one will help her grow a real orchid, so she steals experiment 509, gets it wet, then plants it in a pot with a big dose of super grow for plants. Meanwhile, Stitch trains to ride in the rodeo and Pleakly enters his "Pi-normous," a human-size pineapple. At the competition, Experiment 509 grows to be massive, destroying Pleakly's entry and disrupting the festivities. Lilo and Stitch work together along with Stitch's rodeo completion to get 509 under control and find it's one true home.
Lilo comes up with an alien invasion alarm to improve the hula school, but it was rejected. An experiment makes a loud sonic-blasting noise is so loud that Stitch temporarily loses his hearing. Pleakley goes off capturing Yaarp.
Fed up with Stitch's inflated ego, Jumba activates Stitch's immediate successor, 627, who is much more powerful than Stitch, lacks any of Stitch's weakness, and is so evil that he cannot be turned good.
Lilo and Stitch overhear Gantu's warning of an asteroid that will cause a doomsday. Stitch formulates a plan to go to space and destroy the asteroid to save earth.
Lilo spots a purple dorsal fin luring in the waters while feeding Pudge. Jumba identifies it as an experiment designed to sink ships by slicing them in half.
Nani invites her boss home to demonstrate the spirit of Ohana. Lilo has a crush on Keoni. Before all of that, they found an experiment that is known for snooping around and digging up dirt on the enemy.
Hämsterviel escapes from prison, and the Grand Councilwoman offers Gantu his old captain job back if he can re-capture his current boss for her, while Stitch tries to find Hämsterviel first to upstage an experiment he becomes jealous of.
Lilo hosts a slumber party, but none of her hula classmates want to participate. She comes across an experiment that makes duplicates. When she tried duplicating herself to have her own friends, Stitch got cloned instead after saving her.
Lilo takes Stitch for a carnival, but he's too short to ride on anything. A small crab-like experiment is activated that is known for fouling up machinery.
A small microbe-like experiment enters Pleakley's body, causing a peculiar illness that gives him purple pimples, a swollen eye, extremely smelly feet, and uncontrollable burping. Lilo and Stitch must capture the experiment and remove it from within Pleakley by shrinking to microscopic size. However, they must act quickly, as their shrinking effect is only temporary, and Pleakley is at risk of exploding if they do not make it out of him in time.
Lilo's baseball team is losing due to Pleakley's lack of confidence. She and Mertle make a bet on the next game. A pterosaur-like experiment sports a baseball bat-shaped tail.