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A young Jim Hawkins is enchanted by stories of the legendary pirate Captain Flint and his ability to appear from nowhere, raid passing ships, and disappear in order to hide the loot on the mysterious "Treasure Planet". Twelve years later, Jim has grown into an aloof and isolated teenager, long abandoned by his father. He reluctantly helps his mother Sarah run The Benbow Inn and derives amusement from "Alponian solar cruising", a hybrid of skysurfing and windsurfing atop a board attached to a solar sail-powered rocket.
One day, a spaceship crashes near the inn. The dying pilot, Billy Bones, gives Jim a sphere and tells him to "beware the cyborg". After this, a gang of pirates raid and burn the inn. Jim, his mother, and their dog-like friend Dr. Delbert Doppler flee. At Doppler's study, Jim realizes that the sphere is a holographic projector, showing a star map that leads to the location of Treasure Planet.
Doppler commissions a ship called the RLS Legacy, on a mission to find Treasure Planet. The ship is commanded by the cat-like, sharp-witted Captain Amelia along with her stone-skinned and disciplined First Mate, Mr. Arrow. The crew is a motley bunch, secretly led by the half robot cook John Silver, who Jim suspects is the cyborg of whom he was warned. Jim is sent down to work in the galley, where he is supervised by Silver and his shape-shifting pet, Morph. Despite Jim's mistrust of Silver, they soon form a tenuous father-son relationship.
During the voyage, the ship encounters a supernova. Jim, while securing all lifelines of all crew members, saves Silver from falling just in time. The supernova then devolves into a black hole, where Arrow dies. The burst of shock waves and maximum engine power enable Amelia to pilot the ship to safety. The crew mourns for the loss of Arrow, and begins to suspect Jim of failing to secure the lifelines. Jim blames himself for the mistake, while in fact Arrow's line was cut by a ruthless insectoid crew member named Scroop.
As the ship reaches Treasure Planet, mutiny erupts, led by Silver. Jim, Doppler, Amelia, and Morph abandon the ship, accidentally leaving the map behind. Thinking that Jim has the map, Silver has a chance to kill Jim, but refuses to do so because of his attachment to the boy. The fugitives are shot down by a mutineer during their escape, injuring Amelia.
While exploring Treasure Planet's forests, the fugitives meet B.E.N., an abandoned, whimsical robot, who says that he has literally lost his mind as part of his brain is missing, and invites them to his house to care for the wounded Amelia. The pirates corner the group here; using a back-door, Jim, B.E.N., and Morph return to the ship in an attempt to recover the map. They defeat Scroop, left aboard as lookout, and obtain the map, but on return, are captured by Silver, who has already captured Doppler and Amelia.
Silver forces Jim to use the map, directing them to a portal that opens on any place in the universe, which Jim realizes is how Flint conducted his raids. Using the map, they open the portal to the center of Treasure Planet, discovering that the planet is really a space station built eons ago that Flint commandeered to stow his treasure. As the pirates prepare to collect the wealth, Jim finds the skeletal remains of Flint, holding the missing component to B.E.N.'s cognitive computer. They reinsert it, and B.E.N. immediately recalls that Flint rigged the planet to explode if the treasure was ever disrupted. Too late, the planet begins to fall apart, taking several of the pirates with it. Silver, trying to hold onto a boat-load of gold, opts to let it go to save Jim. The survivors escape to the Legacy, which is damaged and unable to leave the planet. Jim rigs a makeshift rocket-powered sailboard, and rides ahead of the Legacy towards the portal as the planet collapses around them. At the last moment, Jim sets the portal back to his home world's spaceport, and both he and the Legacy safely clear the destruction.
The remains pirates are imprisoned aboard the ship, while Jim finds Silver has snuck below decks to escape. Jim allows him to go, and Silver asks him to keep Morph, as well as providing him some part of the treasure to rebuild the Benbow Inn, believing Jim will "rattle the stars". Amelia offers to recommend Jim to the Intersteller Academy before returning him to the Montressor Spaceport to reunite with his mother. Some time later, a party is hosted at the rebuilt inn, where Doppler and Amelia, married, have children of their own, and Jim is a military cadet. He looks to the skies and sees an image of Silver in the clouds.
What reaches Treasure Planet?
The ship