On a distant planet, Jim Hawkins (voice of JOSEPH GORDON-LEVITT) is a disillusioned teen who's always getting into trouble, much to the dismay of his single mom, Sarah (voice of LAURIE METCALF). She runs the local inn and serves various aliens including Doctor Delbert Doppler (voice of DAVID HYDE PIERCE), an older and somewhat nerdy academic who's taken a liking to her and Jim.
Jim thinks his life is going nowhere, but that changes when a spaceship bearing Billy Bones (voice of PATRICK McGOOHAN) crashes by the inn. The dying spacefarer warns Jim of a cyborg who he doesn't want to acquire the mysterious orb he carries. It's not long, however, before a band of space pirates arrive looking for Bones and that sphere, and Jim, Sarah and Delbert barely escape with their lives.
Jim eventually manages to open the orb that reveals an interstellar map leading to the legendary Treasure Planet that reportedly contains the collective booty of thousands of plundered planets. Since Jim has dreamed of finding the planet since he was a kid, he decides he's going to use the map to get there.
An adventurous boy at heart, Doppler decides to accompany him and charters the RLS Legacy, a space galleon commanded by Captain Amelia (voice of EMMA THOMPSON) and her second-in-command, Mr. Arrow (voice of ROSCOE LEE BROWN). Amelia decides that Jim needs supervision, so she pairs him with John Silver (voice of BRIAN MURRAY), the friendly and weathered cook.
Jim is immediately suspicious of him due to his robotic body parts, but Silver and his little space friend, Morph, quickly allay his doubts and the three become fast friends, particularly when Silver acts as a surrogate father of sorts to Jim.
Yet, things aren't all smooth sailing. After losing a man overboard during a storm, most of the crew, including the monstrous Scroop (voice of MICHAEL WINCOTT), mutiny. Jim, Doppler and Amelia manage to escape the ship and eventually meet B.E.N. (voice of MARTIN SHORT), a chatterbox of a robot who has no long term memory. As they try to figure out what to do next, they must contend with the mutinous pirates and try to get to Treasure Planet before they do.