In order to ensure that no one would be able to find his treasure, Captain Flint murdered his entire crew (the fifteen men he had brought with him to bury his loot) in cold blood after they had buried his treasure. It is then said that the murderous pirate proceeded to leave the island and sailed off into the open sea.
The exact details of Captain Flint's death was not detailed, leaving it largely up to the imagination if he got away with his numerous crimes.
Muppet's Treasure Island
Captain Flint was only seen during the opening sequence, making a map to his treasure, leading his fifteen men to the cave where they buried the treasure and then killing them all. Once they were all dead, he was last seen walking off to his ship, never to be seen again. He ostensibly died later, entrusting the map to Captain Billy Bones, his former first mate.
Treasure PlanetIn this movie, Captain Flint is still a dangerous pirate; however, he is an alien as opposed to a human. During the opening portion of the movie, he was seen pillaging various ships and was notorious for disappearing without a trace when the pillaging was done.
Apparently, he had stolen Treasure Planet (the hideout where he personally buried his ill-gotten loot) from a highly-developed species of unknown name; correspondingly, he also stole the teleportation expertise that he used to raid ships from the same species. Just like in the book, he trusted the map to Treasure Island to Billy Bones. Also, before his death, he stole the memory chip/brain of his navigator, B.E.N, so that, in the event somebody got lucky and found Treasure Planet without the map, nobody would find the treasure. As a final step, Flint (along with his ship) stayed with his treasure until his death.
Captain Flint is later seen (albiet as a corpse) in the core of Treasure Planet. As soon as B.E.N regains his memory, a trap set by Captain Flint was activated. Flint knew that someone from his old crew would come to steal his treasure, so he set up the planet to self-destruct upon the discovery of the treasure.