On the planet Montressor, 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. He reluctantly helps his mother Sarah run the family's Benbow Inn, and derives amusement from "Alponian solar cruising", skysurfing atop a rocket-powered sailboard.
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 finds 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 Captain Amelia along with her stone-skin and disciplined First Mate, Mr. Arrow. The crew is a motley bunch, secretly led by the half-robot cook John Silver, whom Jim suspects is the cyborg 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. Flashbacks are shown in Jim's youth when his father long abandoned him.
During the voyage, the ship encounters a supernova. Jim, while securing lifelines of all crew members, saves Silver from falling just in time. The supernova then devolves into a black hole, where Arrow falls. The burst of shock waves and maximum engine power enable Amelia to pilot the ship to safety. Amelia mourns the loss of Arrow, and suspects Jim of failing to secure the lifelines. Jim blames himself for the mistake, while in fact Arrow's line was cut by a ruthless insectoidcrew member named Scroop.
As the ship reaches Treasure Planet, Jim overhears that the crew are pirates, and mutiny erupts. Jim, Doppler, Amelia, including Morph abandon the ship, but Morph had the map left behind. Thinking that Jim has the map, Silver had a chance to blast Jim, but hesitates 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 robot, who says he has literally lost his primary memory, and invites them to his place for shelter. 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 attacks them, but gets drifted into space. They obtain the map, however on return, are caught by Silver, who already captured Doppler and Amelia.
Silver forces Jim to use the map, directing them to a portal that opens on any location in the universe, which Jim realizes is how Flint conducted his raids. 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. He reinsert it, and B.E.N. immediately recalls that Flint rigged the planet to explode upon the treasure's discovery. The planet begins to fall apart. 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 is unable to leave the planet in time. Jim rigs a makeshift rocket-powered sailboard, and rides ahead of the Legacy towards the portal. At the last moment, Jim sets the portal back to Montressor Spaceport, both he and the Legacy safely clear the destruction.
Jim finds Silver has snuck below decks to escape. He 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 Jim a recommendation to Intersteller Academy before returning to the spaceport to reunite with his mother. Sometime later, a party is hosted at the rebuilt inn, where Doppler and Amelia are married, have children of their own, and Jim is a military cadet. Jim looks into the skies and see an image of Silver in the clouds.
- Team Griffin/Eeveelution, The Griffin Family, Vinny Griffin, Glenn Quagmire, Cleveland Brown, Joe Swanson, Doug Funnie, Skeeter Valentine, Roger Smith, Bender Bending Rodríguez, Minerva Mink, Master Shake, Meatwad, Frylock, Pazu, Sheeta, The Crystal Prep Girls, Wubbzy, Widget, Walden, Daizy, Natsu Dragneel, Lucy Heartfilia, Gray Fullbuster, Erza Scarlet, Wendy Marvell, Happy, and Carla guest star in this film.
- Atlantis: The Lost Empire, Doug's 1st Movie, and Treasure Planet are all Disney films.
- Opening/12 Years Later
- Jim's troubles/Billy Bones
- The map
- Boarding the Legacy
- The Legacy takes off
- Encounter with Scroop/Silver's meeting
- Silver warms up to Jim/"I'm Still Here"
- Jim and Silver's conversation
- Black Hole!
- Silver comforts Jim
- Jim discovers the truth/Treasure Planet!
- Escaping the Legacy/crash landing
- Meeting B.E.N.
- Jim and Silver's argument/sneaking out the back door
- Sneaking back on the Legacy/Scroop's death
- The trail of the treasure
- The portal/Discovery of the treasure!
- The planet's explosion/Silver saves Jim
- Escaping from Treasure Planet
- Silver leaves/Ending
- I'm Still Here - John Rzeznik
- Always Know Where You Are - BBMak (for the end credits)