Unlike how it appears in the first two films the ship has a darker tone as the colors are now red and black stripe sails and a large codfish figure head replacing the skull one from the films.
Roles in the series
The Jolly Roger first appeared in the episode "Hide the Hideout!",Skully warns Jake and the other that the Jolly Roger is coming to Pirate Island. Captain Hook was determined to uncover the young pirate's hide out and make it his own.After several failures and being cast back into the Never Sea by Jake and his crew efforts to keep Hook at bay, the captain catches a cold.With the assistance of Mr. Smee Captain Hook return back to the Jolly Roger to treat his illness.
In the episode "The Old Shell Game", After Izzy discovers a pink polka-dotted shell on Pirate Island beach, she decides to put it on display in her shell collection. Captain Hook also desires the polka-dotted for his own collection,Hook swoop in stealing the shell and fleeing back to the Jolly Roger with Jake and his crew in pursuit with Bucky.
In the special episode Jake and the Never Land Pirates: Peter Pan Returns, Peter Pan's Shadow visits the Jolly Roger: the ship of the villainous Captain Hook. There, he bothers Hook and his crew by awakening them from their slumber.Later the shadow reveals itself. This alerts Hook and his crew of Peter's presence in Never Land. The captain plots to capture the shadow and use it as hostage to lure Peter to him. However, the shadow proves to be elusive as a chase leads the pirates to be thrown overboard and the Jolly Roger to be taken over by the shadow.
In the special episode Jake and the Never Land Pirates: Jake Saves Bucky, Captain Hook can't sleep and wants Sharky, Bones, and Mr. Smee to read a book to him. But Hook doesn't want to hear any of the stories his crew suggests. Hook wants a story about excitement, so the others keep looking. Mr. Smee finds a books that hadn't been touched in quite a while and dusts it off, and coughs afterwards. Smee notices it's one he hasn't seen before - but it wasn't a book, it was a piece of paper.
Hooks wonders what Smee is up too, wanting to know if it is a story worthy of his time. Smee thinks Hook hasn't heard of the story before. Before Smee can read it, Hook grabs it out of his hand. He reads the paper, and reads that The Buccaneer need to take in a race against The Jolly Roger. It also has to start the day after the first full moon of the year. Sharky notices that it would be the next day. If Bucky lost the race, ownership would go to Hook. However, there is still more to read on the paper. It says that Jake and his mates have one last chance to get the ship back. Smee accidentally rips the bottom of the paper and Hook gets it and reads what was on the small part of the paper. Hook thinks it's not important at all. Bones wonders what the race means for them, and Hook says that if his crew wins, Bucky will belong to Hook. Smee thinks that Bucky might not be easy to win in the race, since he has lots of gizmos aboard. Hook then wants new gizmos added to The Jolly Roger. The three crewmen then get ready to build the gizmos for Hook. The next morning, all for prepare for the race and sing a song about having Bucky belonging to Hook. Hook uses every trick in the book and wins the race! But, Jake and his crew might have a way to get Bucky back. With the help of Peter Pan, the young pirates embark on an adventure across Never Land that includes getting past a fire-breathing dragon! With your help, Jake’s crew can save Bucky from the devious Captain Hook.
In the episode "Jake and Sneaky Le Beak!," Captain Hook and his crew plan to set sail for Rainbow Falls to find the Splendor Gem. Hook is interrupted by a falcon that swoops down and swipe Captain Hook's hat off his head who was quickly recognized by Mr. Smee as Beatrice Le Beak pet, knowing that Le Beak can't be far behind. Beatrice then appeared by rowboat claiming her ship was wreck, Captain Hook grants Beatrice permission to come aboard when she over hears Hook and his crew going on a treasure hunt for the Splendor Gem she takes commands of Hook's vessel the Jolly Roger leaving Hook, Smee, Sharky and Bones a drift in her rowboat. Luckily, Jake and his crew were sailing nearby and decided to help. Reluctantly Hook excepts the puny pirates help and gave chase to Rainbow Falls were Beatrice Le Beak has abandon ship leaving Fast Claw to watch the ship but the fiendish falcon is tricked by Skully to leave his post allowing Hook and his crew to take command of the Jolly Roger once more.