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The Jolly Roger is the pirate ship that serves as the home of Captain Hook, Mr. Smee, and their crew. As Hook's base of operations, it is the only place in Neverland that can be considered "pirate territory" (other than Skull Rock).
The ship is first seen in Peter Pan during the part where the Pirate Crew is first introduced. Hook then notices Peter and his gang on one of the clouds as he orders his crew to get their cannons ready to take them down to which they were able to dodge the cannonballs. Later when Peter, the Lost Boys, Wendy, John, and Michael scared off the pirates (when Peter Pan fights Hook and wins), 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. A cloud shaped like the Jolly Roger is seen at the very end of the film during the reprise of "You Can Fly" where George and her wife look at the night sky to which it reminds George of his childhood.
It is last seen in Return to Never Land, 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 recovered 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 abandoned). 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 afterward.
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.
Originally referred to by the name Jewel of the Realm is headed by Captain Liam Jones. On orders of the king, he and his crew are to travel to a distant island and procure a medical plant, Dreamshade, which is rumored to heal all wounds. For the journey, Liam brings his brother, Leftenant Killian Jones. Upon their arrival on the island of Neverland shore they meet a boy named Peter Pan who warns them that Dreamshade is poisonous and comments that their king must be really ruthless, Liam does not heed the boy's warning, while Killian begins to think the king wants the plant to poison his enemies.
After finding the plant Liam purposely wounds himself with the Dreamshade to prove his brother wrong. While nothing happens immediately, Liam soon collapses by the rapidly spreading poison Pan appears to Killian and gives him access to a spring, which will heal his brother, but comes with a price if they choose to leave the island. Liam is healed and they venture off the island with plans of revealing their king's true nature in sending them on the expedition. Once out of Never Land's waters, Liam collapses dying in Killian's arms the price of leaving Never Land's seas. Killian buries his brother at sea. Fueled by anger and a sense of justice, he takes his place as captain, convinces the crew to renounce the king by telling them the truth, and they all take on the life of pirates while the Jewel of the Realm is renamed the Jolly Roger.
In season 3, the Jolly Roger is seen a few times but plays quite a big part in the finale of the season, "There's No Place Like Home". When Killian and Emma are transported back in time, they must find a way onto the Jolly Roger so Emma tries to seduce past Hook. Present Hook sneaks onto the ship to find a way back into the future whilst Emma and a very drunk past Hook are about to have a passionate night together. Emma distracts past Hook by making out with him, which makes present Hook jealous. Killian knocks out past Hook. Back in the present, Killian later trades his ship for Emma to keep her safe. Touched, Emma kisses Hook and they enter a relationship.
The Jolly Roger is later mentioned a few times in other seasons. When Emma and Killian are engaged, he suggests that they marry on the ship until Henry points about the possiblity of the guests vomiting over the edge. The ship is again seen in the season 7 premiere. Newlyweds Emma and Killian are briefly aboard the ship.
The Jolly Roger is the primary setting for the Never Land level in Kingdom Hearts, Kingdom Hearts: Chain of Memories and Kingdom Hearts 358/2 Days. It is also shown that the ship is capable of traveling between worlds of its own accord without the need of a Gummi Ship, as seen when it intercepts Sora's Gummi Ship en route to Never Land along the route from either Halloween Town or Atlantica, with Hook's crew, save for Smee, replaced by Pirate, Air Pirate, and Battleship Emblem Heartless under Hook's command. Even after Hook is defeated and chased off by Tick-Tock the Crocodile, the ship can be revisited to collect any missed chests, Trinity Marks, and in the Final Mix version of Kingdom Hearts, fight the rare Jet Balloon Heartless and its Missile Diver Heartless for rare synthesis items.
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.