Dr. Doppler hired the ship and its crew and remained in the docks of Crescentia Spaceport. (Little did Dr. Doppler know that the crew he hired were all in fact pirates.)
The Legacy took flight and began its journey to find Treasure Planet. On this journey, she was under the command of Captain Amelia with Mr. Arrow as first mate, John Silver as the cook and Jim Hawkins as the cabin boy. Tragically, Mr. Arrow was lost when the ship encountered a Black Hole, however she did make it to her destination.
After Jim became aware of John Silver's plan, the Pirates mutinied and raised their colors. Jim, Doppler, Morph, and Amelia managed to escape to the planet's surface, but the Pirates took pursuit, leaving Mr. Scroop in charge of the ship.
Since the Map was still on the ship, Jim, Morph, and the robot B.E.N. sneaked back aboard and got it back. However, they encountered Scroop, but managed to defeat him when Jim sent him out into empty space.
Amelia and Doppler regained control of the ship and tried to make their escape as the planet began to self destruct. However, the ship suffered severe damage and their chances of escape were in doubt. Jim managed to get the ship and crew out of danger by going through the portal and safely returned to Crescentia Spaceport.