While Jake's crew is having lunch, and after saying, "Never Land Forever!", his sword mysteriously vanishes. The crew learns from Fairy Rock that Never Land is in danger of disappearing forever. The crew begins their quest to save Never Land.
While the crew is on their adventure, Izzy's pixie dust and the pictures on Cubby's map vanish as well. When all hope seems lost, a mysterious guardian appears to Jake, Izzy, and Cubby, and tells them that a quest must be completed in order to save it. The crew is willing to take on the challenge, but the guardian says only one of them can save Never Land. Jake decides to take on the quest, and taking Izzy's pixie dust and Cubby's map with him, sets off to find and restore the magical Forever Tree, the power of which sustains all of Never Land.
Izzy, Cubby and Skully return to Pirate Island, they discover that Captain Hook and his crew are on Pirate Island digging up the place looking for treasure. Izzy, Cubby, and Skully do everything they can to stop Captain Hook.
Meanwhile, Jake follows a small flying light as he completes his quest. First, he goes to the almost-empty Fountain of Forever and gets more pixie dust. Then following the little light to Mermaid Lagoon, Jake learns from Marina and Stormy, that the magical ink from the Golden Squid will restore Cubby's map. When Jake gets to the door to the Forever Tree, he uses a medallion the guardian gave him to open the door. He gets a new golden sword from the old tree, and then the tree disappears.
Meanwhile, the rest of Jake's crew has finally gotten rid of Captain Hook, just in time for the small flying light to find them and lead them to Jake and the guardian, who need their help to make a new Forever Tree grow. They scream, "Yo Ho, Forever Tree Grow!" continuously, and a new Forever Tree grows, the magic is restored, everything reappears, and Never Land is saved!
The guardian reveals himself to be Peter Pan, and the small flying light is revealed to be Tinker Bell. Peter Pan gives Jake the power to fly without pixie dust and invites Jake to explore the worlds beyond Never Land. Jake wants to bring the rest of his crew, but only he can go because he completed the quest. He says his final goodbyes to his crew and goes with Peter Pan, and the crew goes back to Pirate Island.
While flying with Peter Pan, Jake has a feeling that his crew may need him and goes back to Pirate Island. Captain Hook has returned, trapped Izzy, Cubby, and Skully in a cage, and taken their Team Treasure Chest. Jake then frees his mates, but Captain Hook traps Tinker Bell and uses her pixie dust on his ship to fly away. Jake and his ship, Bucky, chase after Hook. Peter Pan frees Tinker Bell, while Bucky shoots a water cannon at Hook's ship to make him stop flying. Jake's crew and Peter Pan do, however, forgive Hook's crew for trying to steal Jake's treasure.
Peter Pan still invites Jake to explore the worlds beyond Never Land with him, but Jake decides to stay in Never Land and Pirate Island with the rest of his crew, because they are not just shipmates, teammates, or even friends... they are a family. Peter Pan agrees saying it was meant to be. "Never Land Rescue" ends with Peter Pan making gold doubloons fall from the sky and they have the crew's faces on them.