Set in London, circa 1900, George and Mary Darling's preparations to attend a party are disrupted by the antics of their boys, John and Michael, along with Petra, Beanie, Timmy and Pikatwo acting out a story about Peter Pan and the pirates, told to them by their older sister, Wendy. They are watched under the eyes of Hubie, Marina, Rocko, Splatter Pheonix, Bonkers, Fawn and Buck. The father, who is fed up with the stories that have made his children less practical, angrily declares that Wendy has gotten too old to continue staying in the nursery with them, and it's time for her to grow up and have a room of her own. That night, they are visited in the nursery by Peter Pan himself, who teaches them to fly with the help of his pixie friend, Tinker Bell, and takes them with him to the island of Never Land.
A ship of pirates is anchored off Never Land, commanded by Captain Hook with his sidekick, Mr. Smee. Hook boldly plots to take revenge upon Peter Pan for cutting off his hand, but he trembles at the presence of a crocodile, which consumed Hook’s hand and is eager to taste the rest of him. Hook also forms a plan to find Peter's hideout using the knowledge of Tiger Lily. The crew's restlessness is interrupted by the arrival of Peter Hubie, his friends and the Darlings. Tinker Bell, who is very jealous of Pan’s attention to Wendy, persuades the Lost Boys that Pan has ordered them to shoot down Wendy, which Tink refers to as a “Wendy bird”. Tinker Bell's treachery is soon found out, and Peter banishes her. John, Michael, the bird kids, Buck and Pikatwo set off with the Lost Boys to find the island's Indians, who instead capture them, believing them to be the ones responsible for taking the chief's daughter, Tiger Lily. Buck who had managed to escape the clutches of the indians hurries off to find Hubie and the others.
Meanwhile, Peter takes Wendy, Hubie, Marina, Rocko, Splatter, Bonkers and Fawn to see the mermaids. The mischievous mermaids delight in tormenting Wendy but flee in terror at the sight of Hook, just as Buck arrives to explain that the kids and Pikatwo are in danger. They see that Hook and Smee have captured Tiger Lily, so that they might coerce her into revealing Peter's hideout. They free her, and Peter is honored by the tribe. Hook then plots to take advantage of Tinker Bell's jealousy of Wendy, tricking her into revealing the location of Peter's lair. Wendy and her brothers eventually grow homesick and plan to return home, along with Hubie and the others. They invite Peter and the Lost Boys to return to London and be adopted by the Darling parents. The Lost Boys agree, but Peter is so set against growing up that he refuses, presumptuously assuming that all of them will return shortly. The pirates lie in wait and capture the Lost Boys, Hubie, his companions and the Darlings as they exit, leaving behind a time bomb to kill Peter. Tinker Bell learns of the plot just in time to snatch the bomb from Peter as it explodes.
Peter rescues Tinker Bell from the rubble and together they confront the pirates, releasing everyone before they can be forced to walk the plank. Peter engages Hook in single combat as the others fight off the crew, and finally succeeds in humiliating the captain. Hook and his crew flee, with the crocodile in hot pursuit. Peter gallantly commandeers the deserted ship, and with the aid of Tinker Bell's pixie dust, flies it to London with everyone aboard. However, the Lost Boys decide to return to Never Land rather than be adopted in London. Mr. and Mrs. Darling return home from the party to find Wendy not in her bed, but sleeping at the open window. Wendy awakens and excitedly tells about their adventures. The parents look out the window and see what appears to be a pirate ship in the clouds. Mr. Darling, who has softened his position about Wendy staying in the nursery, recognizes it from his own childhood.