After capturing all 625 of Jumba's genetic experiments, Stitch, Jumba, and Pleakley are approached by the Grand Councilwoman of the Galactic Alliance with an offer to become part of the Alliance's formidable team of aliens. Stitch declines the offer, as he realizes that Lilo and the rest of his ohana are on Earth and that's where he truly belongs.
Meanwhile, Lilo struggles with the fact that Stitch may one day leave her for his alien family. She also worries about the future of her hula group as most of her friends are moving away.
However, the situation takes a turn for the worse when an evil former experiment named Leroy escapes from his prison asteroid and heads to Earth to cause chaos. When Lilo and the others encounter him, they are outnumbered and outmatched.
In a last-ditch effort to save Earth, Stitch decides to call upon his fellow experiments, who he has reformed and found homes for, to come to their aid. With their help, Lilo and the gang are able to defeat Leroy, but it becomes clear that Stitch's family is in need of his help to keep the galaxy safe.
Despite their sadness at the prospect of being separated, Lilo and Stitch come to understand that sometimes ohana means understanding when it's time to say goodbye. Stitch and his newly formed squad of experiments leave with Jumba and Pleakley to travel the galaxy and help others, but Lilo remains behind on Earth as the leader of her hula group and with her own place in the world.