Captain Flynn is the most famous pirate to ever sail the Never Sea, much to Captain Hook's dismay. To pirates, and the inhabitants of Neverland altogether, Flynn is viewed as a heroic celebrity having several fans and admirers. He sails brilliantly across both land and sea on his mechanical ship The Barracuda, which has built-in wheels that activate when on a terrain. He is accompanied by his loyal camel companion Camille.
In the episode Pirates of the Desert, it is a windy day in Never Land and the wind blew various things onto a tree on Pirate Island. Skully discovers a piece of paper that is actually a note of help sent by Captain Flynn who is trapped in the Never Desert. The crew travels there to find a camel. The camel belongs to Flynn and is named Camille. Flynn asks the crew to help find his ship which he lost when he was shipwrecked. The wreck also wiped out Flynn's memory. He remembers a few things which Izzy and the crew use to retrace the steps of Flynn. Eventually, they recover the ship but Captain Hook and Smee are there first. Hook claims the ship as his own and plans on taking control. Earlier that day, Cubby learned that Camille's way of playing is head budding. So, Jake asks Camille to play with Hook, knocking the captain and Smee off the ship. Izzy then uses pixie dust on the ship to fly over to Pirate Island where Flynn and Camille decide to stay until the ship is repaired.
The next episode The Great Pirate Pyramid, Flynn finds a broken map piece in his ship's quarters. Cubby quickly understands the map and tells the crew that it leads to The Great Pirate pyramid. With the ship repaired, they set sail. While out in the Never Sea, Sharky, one of Hook's crew members, reveals his talents to read lips and begins to read those of Izzy and Cubby using a telescope to see up close. He does so successfully having Hook wanting to find the pyramid. Once they reach their destination, Camille finds the complete map and connects the broken piece. The map becomes a moving painting and reveals that the pyramid is available to be a hideout to a great pirate and is able to hold a ship inside. Flynn decides to reside at the pyramid and loads in The Barracuda. Jake, Izzy, Cubby, and Skully bid Flynn a farewell.
Captain Flynn reappears in the episodes "Tricks, Treats and Treasure!" and "Captain Flynn's New Matey". Captain Flynn attended Jake's birthday celebration with the rest of the pirate teams Never Land friends in "Jake's Birthday Bash!"
In the episode Song of the Desert, Sharky and Bones have invited Flynn to perform in a concert held in Never Land which in reality was a scheme cooked up by Captain Hook to lure Flynn from the pyramid allowing Hook and Smee to raid the pyramid for treasure.
Captain Flynn reappears in the episode Treasure of the Pirate Mummy's Tomb his ship The Barracuda get stuck within the sand of the sands of the Never Land Desert when Jake and his crew come to Flynn's aid revealing only the golden ankh has the power to free The Barracuda from the sand located in the Pirate Mummy's Tomb.
Captain Flynn makes a brief cameo in the episode "Jake's Pirate Swap Meet", it is unclear if he sold or purchases anything from the Pirate Swap Meet.
Captain Flynn makes a nonspeaking cameo in the episode "Smee-erella" attending Red Jessica's pirate convention he could be seen conversing with Misty the Wonderful Witch. Later, the two are seen dancing during the pirate waltz. Flynn is last seen sailing his ship in the pirate ship parade.
Captain Flynn makes a reappearance in the episode "Cubby's Tall Tale", sharing his various pirate tales with his young mateys on Shipwreck Beach. Once it became Cubby's turn to tell a tale. Cubby exaggerates his tall tale about his buried treasure at the top of Hidden Peak Captain Hook overhears and sets off to find it taking Cubby's map. Jake and his crew accompanied by Flynn give chase after Hook but once they reach the river Jake and his crew went ahead. Flynn later reappears to confront Hook and his crew with the assistants of his fire belching friend Belchy the dragon forcing Hook and his crew to flee leaving the treasure.
- "Pirates of the Desert" (first appearance)
- "The Great Pirate Pyramid"
- "Tricks, Treats and Treasure!"
- "Captain Flynn's New Matey"
- "Jake's Birthday Bash!"
- "Sand Pirate Cubby!"
- "Song of the Desert"
- "Treasure of the Pirate Mummy's Tomb"
- "Jake's Pirate Swap Meet"(cameo)
- "Smee-erella" (cameo)
- "Cubby's Tall Tale"
- "Captain Scrooge"
- "Jake's Awesome Surprise"