The film opens on a young Jim Hawkins (Joseph Gordon-Levitt), reading a holographic book on the space pirate, Captain Nathaniel Flint who stores his booty on the legendary "Treasure Planet."
Jim is now a rebellious 15 year-old, with a knack for mechanics and engineering his own "solar surfers" (a sci-fi analog to wind surfing). One night, an old "spacer" (i.e. space sailor) named Billy Bones lands by the Hawkins family inn, but is in poor shape. He gives Jim a golden ball, a map to Captain Flint's treasure and warns Jim about a cyborg. Bones then dies and the inn is ransacked and burned by pirates as Jim and his mother escape with family friend, Doctor Delbert Doppler (David Hyde Pierce).
Doctor Doppler fiances a voyage to find Treasure Planet, hiring a ship and crew including Captain Amelia (Emma Thompson), her first mate Mr. Arrow (Roscoe Lee Browne), and the cyborg cook, Long John Silver (Brian Murray). Jim is assigned to be Silver's cabin boy; although initially suspicious of the cook (who is indeed a pirate captain in disguise), the two quickly form a strong bond. Silver becomes a father figure for Jim and helps Jim find purpose and meaning to what he does. However, when traversing space, the ship encounters many dangers. At one point, Jim is responsible for securing lifelines for the whole crew, which he does successfully, but Scroop (Michael Wincott), a sinister member of the crew and one of Silver's coherts, disposes of Mr. Arrow. Jim blames himself when the life line is missing. Silver knows that Scroop is responsible and tries to comfort Jim.
Soon they are in sight of Treasure Planet and the pirates plan to mutiny. Silver, worried about seeming soft, also denounces his relationship with Jim as nothing. Jim overhears all of this and informs the captain. The mutiny begins and the captain, Dr. Doppler, and Jim flee to the planet surface. While there, Jim finds a robot named B.E.N. (Martin Short), a member of Flint's crew left there because he knows (but has forgotten) the secrets of the planet. The Captain and Dr. Doppler are captured by Silver and the pirates, so Jim agrees to lead the pirates to the treasure. They find a portal that can open to any corner of the universe, including the interior of the planet where the treasure is hidden. However, the crew sets off a booby trap that begins to destroy the planet. Dr. Doppler and the Captain retake the ship, and Silver saves Jim, sacrificing the treasure he had been searching for. Jim, Silver, the Doppler, and the Captain use the portal to escape the exploding planet. Silver, then flees to avoid jail, with Jim's blessing. Silver leaves Jim a handful of treasure to rebuild the family inn.
Captain Amelia recommends Jim to the Interstellar Academy; in the epilogue the inn is rebuilt and Jim has matured in an upstanding young man.