About Cartoon: The film's prologue depicts Jim Hawkins as a three-year-old (voiced by Austin Majors) reading a storybook in bed. Jim is enchanted by stories of the legendary space 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 (now voiced by Joseph Gordon-Levitt) has grown into an aloof 15-year-old. He is shown begrudgingly helping his mother Sarah (Laurie Metcalf) run an inn and deriving amusement from "solar surfing" (a hybrid of skysurfing and windsurfing atop a board attached to a solar-powered rocket), a pastime that frequently gets him in trouble for using it in a restricted area.
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. The sphere turns out to be a holographic projector, showing a map that Jim realizes leads to Treasure Planet.
Doppler commissions a solar galleon called "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), whom Jim suspects is the cyborg of whom he was warned. Jim is sent down to work in the galley; despite his mistrust of Silver, they soon form a tenuous father-son relationship (a montage featuring the song "I'm Still Here" shows Jim and the cyborg bonding over various sailing chores, interspersed with flashbacks from Jim's childhood, during which his father appears indifferent to him and finally leaves without warning when Jim is a pre-teen). During an encounter with a black hole, Arrow drifts overboard and is lost, for which Jim blames himself for failing to secure the lifelines, 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, and Amelia 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 and B.E.N. 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. Jim grabs the mast while Scroop becomes entangled in the flag and cuts himself free while Scroop floats away, presumably to his death. Jim and B.E.N. 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 decides to save 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, inheriting Silver's shape-changing pet called Morph (Dane A. Davis). 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 inn. The film ends with a party at the rebuilt inn, showing Doppler and Amelia now married with children, and Jim a military cadet. He looks to the skies and sees an image of Silver smiling at him from the clouds.
Jim Hawkins, the protagonist
Long John Silver he anti-hero
Dr. Delbert Doppler
Sarah Hawkins, Jim's mother
Scroop, the antagonist