It is first seen in Peter Pan. When Peter Pan, the Lost Boys, Wendy, John and Michael scare off the pirates, they desert their ship, leaving Peter to temporarily commandeer it. Peter uses it to take the Darlings back home by having Tinkerbell cover it with pixie dust, enabling it to fly.
It is last seen in Return to Neverland, where the pirates are back in control of the ship. During the start of the film, it is apparent that the pixie dust that was used in the first film is still in effect; however, Wendy's story that she tells Jane and Danny states that the ship was covered in pixie dust during a successful treasure theft (courtesy of Peter Pan), which contradicts what occurred in the first film, however, it is very possible that it was re-covered in Pixie Dust or that Wendy just made the story up. The ship is mistaken for a bomber when Jane is kidnapped and Hook and his crew are forced to escape as the Germans attack London. It, again, serves as Hook and his crew's home base (Skull Rock having apparently been forgotten or abandonded). During the end of the film, the Jolly Roger is destroyed when Hook is sent plummeting through several floors of it (with help from a heavy anchor) and crashes into the Octopus, who, having been sent into a rage because of his blunder, destroys the ship all in an attempt to eat Hook alive. It sinks to the bottom of the sea soon afterwards.
The ship also appears in the animated television series serving as the central location for Hook and his crew. Since the original ship was destroyed, the crew was forced to rebuild it apparently wanting to give a darker tone as the colors are now pure red and black.
The Jolly Roger was a Disneyland landmark from its opening to 1983 in the form of the Chicken of the Sea Pirate Ship restaurant in Fantasyland. However, the pirate ship was damaged when being moved during the Fantasyland overhaul and parts of it would be used in Peter Pan's Flight. The tradition of Hook's pirate ship in the parks would live on though at the Disneyland Hotel's Neverland Pool and at Disneyland Paris's Adventure Isle.
The Sailing Ship Columbia plays the part of Captain Hook's ship in the Disneyland Fantasmic
A battered version of Jolly Roger is the location of a boss fight against a robotic Captain Hook. Mickey Mouse must either defeat Hook on the decks by altering the path of his rails to a plank leading to the crocodile or climb up the rigging to release a captured Sprite that will summon Pete Pan to fight on Mickey's behalf.