The game takes place at an unknown point of time after the original film. An extraterrestrial bounty hunter kidnaps Lilo (vocal effects by Daveigh Chase) and brings her aboard the spaceship laboratory of a robotic, mosquito-like alien named Dr. Pestus, who plans to use her as food for his genetically-modified mosquito army. Stitch (vocal effects by Chris Sanders) must go out into space to rescue Lilo and defeat Dr. Pestus. In most levels, the player takes control of a four-armed, plasma blaster-wielding Stitch who must run and gun his way past enemies and various other obstacles to complete the level. He can also acquire special ammunition for his plasma blasters that allow him to fire more powerful plasma blasts and can acquire pineapple bombs to throw at enemies. In a couple puzzle-platform-styled levels, the player takes control of Lilo as she sneaks around the spaceship to find a way to escape and contact Stitch. In a couple tube shooter-styled segments, Stitch must fly a spaceship to reach the next level, shooting down other enemy ships and dodging obstacles along the way.