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The Jolly Roger is a pirate ship.
The Jolly Roger is the pirate ship sailed by Captain Hook, originally in the real world, but later on the Neverseas after he began his campaign against Peter Pan. Though damaged or even sunken many times, the Jolly Roger, like its own captain, always eventually resurfaces. During Wendy Darling and her brothers' first visit to Neverland, the ship, briefly captured by Peter Pan and the Lost Boys, was sprinkled with Pixie Dust by Tinker Bell, which later allowed Hook to fly the ship, to the extant that it afforded him an easy route for moving back and forth between Neverland and Earth.
Behind the scenes
Interestingly, although one might assume the ship is simply named for the infamous flag, a famous pirate called Jolly Roger was confirmed to have existed in the Prime Universe as early as 1942's Donald Duck Finds Pirate Gold. It is possible Hook was familiar with this Jolly Roger and named the ship after him; this would be consistent with the backstory proposed by J. V. Hart for the literary Hook in his prequel novel Capt. Hook: The Adventures of a Notorious Youth, where it was actually Hook himself who bestowed the nickname of “Jolly Roger” to a classmate of his at Eton, Roger Peter Davies.