Soon after Peter, an orphan, sets sail from England on the ship Never Land, he befriends and assists Molly, a young Starcatcher, whose mission is to guard a trunk of magical stardust from a greedy pirate and the native inhabitants of a remote island.
Realizing that Molly and the other Starcatchers are in danger when the sinister being Lord Ombra visits the island and seems to control people through their shadows, Peter and Tinker Bell travel to England to help save the stardust.
James, one of Peter's original Lost Boys, is now working for Scotland Yard and suspects that the heir to England's throne, Prince Albert Edward, is under the influence of shadow creatures who are after starstuff hidden in an underground vault which has only one key: the Sword of Mercy. Molly is determined to help, but when she suddenly goes missing, it's up to her eleven-year-old daughter, Wendy, to keep the starstuff out of the creatures' clutches...
Aidan and Sarah Cooper begin to decipher a mysterious coded document that they discovered in a secret compartment of an antique English desk their father recently bought at an auction, and as they become more involved in the piece, which seems to be referring to the story about the origin of Peter Pan, a powerful being begins to pursue them.