Set in the future, the film’s prologue depicts Jim Hawkins as a five-year-old (voiced by Austin Majors) reading a storybook in bed. Jim 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 (Joseph Gordon-Levitt) has grown into an aloof and alienated teenager, long abandoned by his father. He is shown begrudgingly helping his mother Sarah (Laurie Metcalf) run The Benbow Inn and deriving amusement from “solar surfing” (a hybrid of skysurfing and windsurfing atop a board attached to a solar sail-powered rocket), a pastime that frequently gets him in trouble.
One day, a spaceship crashes near the inn. The dying pilot, Billy Bones (Patrick McGoohan), gives Jim a sphere and tells him to “beware the cyborg”. Shortly thereafter, a gang of pirates raid and burn the inn. Jim, his mother, and their dog-like friend Dr. Delbert Doppler (David Hyde Pierce) barely escape. While at Doppler’s study, Jim realizes that that sphere turns out to be a holographic projector, showing a 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 (Emma Thompson) along with her stony-skinned and disciplined First Mate, Mr. Arrow (Roscoe Lee Browne). The crew is a motley bunch, secretly led by cook John Silver (Brian Murray), 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 (Dane Davis). 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 falls to his death. The burst of shock waves and maximum engine power enable Captain 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 (Michael Wincott).
As the ship reaches Treasure Planet, mutiny erupts, led by Silver. Jim, Doppler, Amelia, and Morph abandon the ship, accidentally leaving the map behind. Silver, who believes that Jim has the map, 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, causing injury to Amelia.
While exploring Treasure Planet’s forests, the fugitives meet B.E.N. (Martin Short), an abandoned, whimsical robot who claims to have lost most of his memory 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. Scroop, aboard the ship as lookout, stalks and fights Jim. B.E.N., working to sabotage the ship’s artillery, accidentally turns off the artificial gravity, whereupon Jim and Scroop threaten to float off into space. Scroop grabs the mast while Jim grabs the flag at the top of the mast. Scroop partially cuts the flag’s halyard, but Jim grabs the mast, and manages to kick Scroop into the flag, breaking the halyard and causing Scroop to float away to his death. Jim and B.E.N. then obtain the map. Upon their return, they are captured by Silver, who has already captured Doppler and Amelia.
When Jim is forced to use the map, the group finds their way to a portal that can be opened to any place in the universe; this being the means by which Flint conducted his raids. The treasure is at the center of the planet, accessible only via the portal. Treasure Planet is revealed to be a large space station built by unknown architects and commandeered by Flint. In the stash of treasure, Jim comes across the skeletal remains of Flint himself, holding a missing part of B.E.N’s cognitive computer. Jim replaces this piece, causing B.E.N. to remember that the planet is set to explode upon the treasure’s discovery. In the ensuing catastrophe, Silver finds himself torn between holding onto a literal boat-load of gold and saving Jim, who hangs from a precipice after a fall. Silver saves Jim, and the group escapes to the Legacy, which is damaged and lacks the motive power required to leave the planet in time to escape. Jim attaches a rocket to a narrow plate of metal and rides it toward the portal to open it to a new location, while Doppler pilots the ship behind him. Jim manages to open the portal to his home world’s spaceport, through which all escape the destruction of Treasure Planet.
After the escape, Amelia has the surviving pirates imprisoned aboard the ship and offers to recommend Jim to the Interstellar Academy for his heroic actions. Silver sneaks below deck, where Jim finds him preparing his escape. Jim lets him go, and Silver asks Jim to keep Morph. Silver predicts that Jim will “rattle the stars”, then tosses him a handful of jewels and gold he had taken from Treasure Planet to pay for rebuilding The Benbow Inn before flying off. Jim returns to Montressor Spaceport and reunites with his mother. Sometime 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.