Doctor Aaron's journey to Treasure Planet

Plot
Set in the future, the film's prologue depicts Jim Hawkins as a five-year-old 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 has grown into an aloof and alienated teenager. He is shown begrudgingly helping his mother Sarah run an 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, after meeting Doctor Aaron and his crew, a spaceship crashes near the inn. The dying pilot, Billy Bones, gives Jim a sphere and tells him and the TARDIS Team to "beware the cyborg". Shortly thereafter, a gang of pirates raid and burn the inn. Jim, his mother, Doctor Aaron Tierney, Cynder, Batty Koda, Wave the Swallow, Juniper Montage, Captain Celaeno, and their dog-like friend Dr. Delbert Doppler barely escape. The sphere turns out to be a holographic projector, showing a map that Jim realizes leads to Treasure Planet.

Doppler commissions a ship called RLS Legacy, on a mission to find Treasure Planet. The ship is commanded by the cat-like, sharp-witted Captain Amelia along with her stony-skinned and disciplined First Mate, Mr. Arrow. The crew is a motley bunch, secretly led by cook John Silver, whom 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 while the TARDIS Team is assigned other miscellaneous tasks. Despite Jim's 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 supernova, Silver falls overboard but is saved by Jim. The supernova then devolves into a black hole, where 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.

As the ship reaches Treasure Planet, mutiny erupts, led by Silver. Jim, Doppler, Amelia, Morph, and the TARDIS Team 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., 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., Morph, Doctor Aaron, Batty Koda, and Captain Celaeno return to the ship in an attempt to recover the map. Scroop, aboard the ship as lookout, stalks and fights Jim and Celaeno. B.E.N. and Doctor Aaron work on sabotaging the ship's artillery when B.E.N. accidentally turns off the artificial gravity, where upon Jim, Celaeno, 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, B.E.N., Doctor Aaron, and Celaeno then obtain the map. Upon their return, they are captured by Silver, who has already captured, bound, and gagged Cynder, Wave the Swallow, Juniper Montage, Doppler and Amelia.

When Jim and Doctor Aaron are 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, in which two of the pirates fall down into the lava and the others escape, 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 (she offers to recommend Doctor Aaron and his crew to the Interstellar Academy as well, they politely decline). Silver sneaks below deck, where Jim and the TARDIS Team find him preparing his escape. They let 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 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 in the clouds.

As for Doctor Aaron and his crew and where they would go from there... Only time will tell.