The Jolly Roger is the pirate ship that serves as the home of Captain Hook, Mr. Smee and their Pirate Crew. It is the base of operations for Captain Hook and is the only place in Never Land that can be considered "pirate territory" (other than Skull Rock).
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 Tinker Bell 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 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.
Although the Jolly Roger is not the main ship that appears in the film it does make a brief appearance at the end during the credits where it rescues it's future Captain from the sea.