During production, the film was known under the working titles Quest for the Queen and Tinker Bell and the Mystical Island.
While most dust-talent fairies are content to simply process, sort, and deliver pixie dust, dust-talent fairy Zarina wants to know more about its possibilities and potential. She defies Fairy Gary's orders to never tamper with dust and conducts experiments in secret, and discovers a process to make dusts that can make any fairy capable of using a talent different than their own. However, an accident in her workshop ends up with the Pixie Dust Distribution Depot severely damaged. Zarina offers to come in early and stay late to help repair the damage, but Fairy Gary tells her not to come back at all, and that she is no longer a dust-keeper. Zarina packs up a few of her things, and leaves Pixie Hollow.
A year later at the Four Seasons Festival, Zarina returns and uses poppies to put the rest of the fairies to sleep at the event. However, she misses Tinker Bell, Iridessa, Rosetta, Silvermist, Vidia, and Fawn, who all hide in an object they were meant to use during the festival's opening ceremony. She also misses Clank, who had gone off to use the outhouse. After the unaffected fairies come out of hiding and see what's happened, Rosetta says that those who have fallen asleep will remain thus for "at least a couple of days."
Tinker Bell, Iridessa, Rosetta, Silvermist, Vidia, and Fawn follow after Zarina while Clank remains in Pixie Hollow to watch over everyone else. Tinker Bell and the others follow Zarina out to the ocean, where they see pirates taking Zarina and the blue pixie dust out to a ship on a rowboat. Tinker Bell decides that the pirates must have captured Zarina and forced her to take the dust, and so she and the others fly out to the rowboat to rescue her. They soon discover that Zarina wasn't captured at all - she is in fact the captain of this pirate crew. Tink decides to simply get the dust and leave. The fairies succeed in getting the blue pixie dust away from the pirates, but Zarina throws alchemized dust at them and knocks them back through a waterfall. She takes the dust back and returns to her crew.
The fairies wake up the next morning and discover that their talents have been switched - Tinker Bell is now a water-talent fairy, Silvermist is a fast-flying-talent fairy, Fawn is a light-talent fairy, Iridessa is a garden-talent fairy, Rosetta is an animal-talent fairy, and Vidia is a tinker-talent fairy. They attempt to leave the area behind the waterfall, and end up washed down to a beach where Rosetta encounters an egg that soon hatches into a baby crocodile. The crocodile imprints on Rosetta, deciding that she is its mother.
Silvermist locates the pirate ship, and the fairies resume their quest to retrieve the blue pixie dust. They reach the ship in time to learn that the pirates had discovered Zarina after drifting into Never Land, that she had promised to make their ship fly, and that the pirates intend to use their flying ship to plunder the world.
The pirates sail to Skull Rock, where Zarina and the pirates take the dust to a tree Zarina grew inside to make their own pixie dust tree. The fairies follow them to the tree to try to get the dust back, but are captured by Oppenheimer and taken down to the galley. Meanwhile, Zarina releases a few grains of dust into the tree, which begins producing pixie dust. James wonders aloud what it would be like to fly, so Zarina takes him for a short fly around Skull Rock with a little pixie dust.
Afterward, James confirms that so long as they have the blue pixie dust they'll be able to continue producing golden pixie dust to make the ship fly. Then he reveals his true colors: he only kept up friendly pretenses with Zarina as long as they needed her help, and now that they have a working tree they no longer need her. James puts Zarina into his fairy lamp and takes her to his cabin, where he puts on his captain's clothes, taking position as Captain James Hook.
Back in the galley, the baby crocodile that imprinted on Rosetta crawls in through a cannon port, and with Rosetta's encouragement helps the fairies get free. The fairies escape the ship and retrieve the blue pixie dust, but are immediately ordered to return it by James, who threatens to kill Zarina if they refuse. Tinker Bell returns the blue pixie dust, and James dusts the ship with golden pixie dust. James takes the blue pixie dust with him and drops the lamp into the water. Tinker Bell and the others rescue Zarina, and together they return to James's ship to battle the pirates for the dust and stop them from escaping Never Land on their now-flying ship.
During the battle, Rosetta chases after Oppenheimer on the crocodile's back. Oppenheimer throws a variety of objects at them to fend them off, including a clock. The crocodile catches the clock in his mouth and swallows it. Oppenheimer falls off of the ship after the crocodile bites his ankle.
Zarina pins James with one of the ship's yards and takes the pixie dust, then turns the ship upside-down to dump the remaining pirates into the sea. James falls beneath the ship's store of pixie dust, and thanks to Zarina's earlier flight lessons he is able to fly after her to get the dust back. However, a single speck of blue pixie dust falls within Zarina's grasp, which she throws at James. The blue pixie dust amplifies the dust already on James, causing him to fly out of control. Tinker Bell raises a wave in front of him which washes off the dust. Just before he falls into the ocean with his crewmates, Zarina snatches the dust away.
The fairies return to Pixie Hollow on the pirate ship, where they wake up the rest of the fairies with a mix of golden pixie dust and garden-talent pixie dust. Tinker Bell informs Queen Clarion that they've brought the blue pixie dust back, and Fairy Gary welcomes Zarina home with a hug. Zarina begins to promise that she'll never tamper with pixie dust again, but Tinker Bell interjects, saying that she has mastered it. Rosetta points out that Zarina even grew a pixie dust tree. Tinker Bell says that they should see Zarina in action, and Queen Clarion points out that they do have an audience.
That night, at the (resumed) Four Seasons Festival, Zarina changes the fairies back to their original talents as they perform by throwing pixie dust at them in front of the audience. Zarina takes a bow with the rest of the fairies.
Later, James is found floating adrift by Smee.
- Mae Whitman as Tinker Bell
- Pamela Adlon as Vidia
- Lucy Liu as Silvermist
- Megan Hilty as Rosetta
- Raven-Symoné as Iridessa
- Angela Bartys as Fawn
- Christina Hendricks as Zarina
- Tom Hiddleston as James
- Jim Cummings as Oppenheimer
- Carlos Ponce as Bonito
- Jim Cummings as Port
- Mick Wingert as Starboard
- Kevin Michael Richardson as Yang
- Jeff Bennett as Smee