Jim Hawkins is a young boy enchanted by tales of the legendary pirate Captain Flint, who hides his stolen treasures on Treasure Planet. Twelve years later, Jim now helps his mother Sarah run an inn, and is frequently in trouble with the law. One day, Jim is given a sphere by a dying pilot, Billy Bones. Shortly afterwards, the inn is destroyed by pirates.
Jim and his mother stay at Dr. Delbert Doppler's study, where Jim discovers that the sphere is a holographic projector which reveals the location of Treasure Planet. Jim and Doppler join a ship called the RLS Legacy, commanded by Captain Amelia, along with her First Mate, Mr. Arrow. Jim is sent to work in the gallery, supervised by the ship's cook, John Silver, and his shape-shifting pet, Morph. On the voyage, the ship encounters a supernova, which devolves into a black hole. Mr. Arrow is killed when one of the crew members, Scroop, severs his lifeline, causing him to be sucked into the black hole.
As the ship reaches Treasure Island, Silver leads a mutiny. Jim, Doppler, Amelia, and Morph abandon the ship, leaving behind the sphere, but Amelia is injured. Now fugitives, the group venture through Treasure Island's forests, where they meet B.E.N., a robot who has lost part of his memory. He invites the fugitives to stay at his house. As the pirates arrive, Jim, B.E.N., and Morph enter the ship to retrieve the sphere. Scroop attacks Jim, but B.E.N. deactivates the artificial gravity, causing Scroop to float of into space. Jim and B.E.N. return to the house, but they are captured by Silver. Jim is forced to use the sphere to find a portal, which Captain Flint had used on his pirate raids. They discover that the treasure is located at the center of the planet, accessible only by the portal.
Jim discovers Treasure Planet to be a massive space station, and finds Flint's remains. He recovers a missing piece of B.E.N.'s cognitive computer, which restores his memory. B.E.N. remembers that Treasure Planet is set to explode upon the treasures discovery. In the ensuing chaos, during which the pirates are forced to disband, Silver rescues Jim. They return to the Legacy, which has been damaged, disabling it from leaving the planet in time. However, Jim manages to open the portal to his planet's spaceport, allowing everyone to escape from Treasure Planet as it explodes.
Amelia has the remaining pirates imprisoned and offers Jim a place in the Interstellar Academy. Jim notices Silver attempting to escape, but lets him go. Silver asks Jim to keep Morph and gives him a handful of stolen gold to pay for the destroyed inn before he flies off. Some time later, a party is hosted at the rebuilt inn, and Jim has become a military cadet while Amelia and Doppler marry. Jim looks into the skies and sees an image of Silver in the clouds.
- Joseph Gordon-Levitt as Jim Hawkins.
- Brian Murray as John Silver.
- Emma Thompson as Captain Amelia.
- David Hyde Pierce as Delbert Doppler.
- Martin Short as B.E.N.
- Patrick McGoohan as Billy Bones.
- Dane A. Davis as Morph.
- Roscoe Lee Browne as Mr. Arrow.
- Laurie Metcalf as Sarah Hawkins.
- Michael Wincott as Scroop.
- Michael McShane as Hands
- Corey Burton as Onus
- Jack Angel as Schwartzkopf, Robocop #2
- Rodger Bumpass as Mr. Turnbuckle, Robocop #1
- Mickie McGowan as Birdbrian Mary
- Phil Proctor as Meltdown