Slightly visits the "oracle" of Neverland wishing to be Peter's second in command, which he is eventually appointed to. After being much too naive and getting tricked first by his friends, as a joke, and later by the pirates, more seriously, he causes a lot of trouble for everybody and finally realizes he's not qualified for the position.

The Twins, sick of being so closely associated with one another, begin fighting incessantly. Their riff coincides with the preparations for a race around the island that everyone - including the pirates - wants to win. The Twins try to beat each other in building the fastest racing machine but wind up creating the same design. The Great Race finally arrives but is nearly ruined by the fierce competition between Peter, the Lost Boys, and the cheating pirates. In the end, the Twins resolve their differences and work together to save their friends, while Michael wins the race riding only a tricycle.

Responding to Peter's complaints that Wendy's stories aren't exciting enough, Tinker Bell enchants the pages of Wendy's book so that the story comes alive as it's told. Anyone who's in the story must enact the action and obey all the narration; this applies to Peter since he's the hero of the story. It's not long before word of this soon reaches the Jolly Roger and Hook devises a plan to steal its pages. Once he succeeds, he begins rewriting the story so that Peter cannot fly or fight and the Darlings and Lost Boys are helpless captives. Things take a turn for the better when Wendy is able to reach the stolen pages and write the Crocodile into the story.

Peter takes the hat from Hook and suddenly thinks to be the Captain himself. Disappointed of the big defeat Hooks leaves the Jolly Roger and now the Pirates have to look after themselves. Mullins decides to become the new Captain and tries to take back the pirate's hat from Peter, but because of his landsickness he is too weak to fight outside the ship, so Peter beats him and soon has the control of the pirate crew and the Jolly Roger, where he moves with the Boys. Wendy knows this won't end good so she decides to find Hook, who she wants to return and bring everything back to normal.

Peter and Tink sneak on board the Jolly Roger in order to play with Hook's harpsichord. Hook catches them in the act and captures Peter, destroying his beloved instrument in the process. All looks grim for Peter until Wendy flies over and convinces Hook to give Peter a trial. But is a fair trial and a just outcome even possible when the entire court is comprised of pirates?

After taking a hit in the head, Captain Hook believes he is Dr Livingstone.

Captain Hook steals the Neverscroll and starts erasing Neverland.

Peter and the Lost Boys cause a commotion among the pirates when they steal the Jolly Roger's flag. In trying to retaliate, Hook puts too much gunpowder into Long Tom and gets blown to smithereens. The rest of the pirates decide to leave Neverland since their captain's vendetta with Peter was the only thing that kept them there. Peter is devastated that Hook is dead and the pirates are gone. But he may just get one last showdown with his archenemy when the Lost Boys tell him that Hook's ghost now haunts a cave.

Hook injures himself while trying to capture Peter Pan and Wendy insists they take care of him until he's well again.

Hook tampers with Great Big Little Panther's magic, sending the weather of Neverland into a frenzy. Peter must retrieve the magic sand before the storms Hook created kill anyone.

When Smoky Top begins to rumble menacingly, Peter and the Lost Boys go to see Great Big Little Panther for help. However, the shaman has gone on a retreat, so Hard-to-Hit attempts shaman magic to call forth a vision of what is to come from the sacred flames. He deciphers that Neverland is about to be destroyed. Peter sets about warning everyone in Neverland while the lost boys evacuate the Underground House. Wendy brings up the fact that not all the animals can fly away, so Peter decides that Hook's ship will have to suffice as an Ark to carry the animals to safety.