Zarina (Christina Hendricks), a very smart and inquisitive pixie dust-keeper fairy, is amazed by the magic behind pixie dust and is determined to find out all that it is capable of. After her secretly experimenting with some blue pixie dust and causing an accident in Pixie Hollow, her supervisor Fairy Gary prohibits her from being a dust-keeper. In sorrow, Zarina takes her experiments and runs away from Pixie Hollow.
One year later, Pixie Hollow celebrates the Four Seasons Festival, with performances from fairies of all the seasons. During the show, Tinker Bell (Mae Whitman), Silvermist (Lucy Liu), Iridessa (Raven-Symoné), Rosetta (Megan Hilty), Fawn (Angela Bartys), and Vidia (Pamela Adlon) spot Zarina flying around the audience and using some strange pixie dust to summon several poppies that cause everyone to fall asleep, except Tink and her friends who take cover. After Zarina is gone, they realize that she stole all of the blue pixie dust, the only way to make the yellow dust that the fairies use to fly, so they go after her to return it to its rightful place.
They follow Zarina to the coast, where it is revealed that she became the captain of a pirate crew, including the cabin boy, James Hook (Tom Hiddleston). The fairies manage to retrieve the blue dust for a moment, but Zarina gets it back after throwing at them some multicolored pixie dust that magically switches their innate fairy abilities and talents. Tinker Bell becomes a water fairy, Silvermist becomes a fast-flying fairy, Fawn becomes a light fairy, Iridessa becomes a garden fairy, Rosetta becomes an animal fairy, and Vidia becomes a tinker fairy, much to her horror and disgust. They struggle with their swapped talents as they search for Zarina and the pirate ship, in the process meeting a baby crocodile which takes a liking to Rosetta. They find the ship and sneak in, where they hear James saying how the pirates met Zarina after drifting off course, and she became the captain with the promise of making the ship fly so that they could plunder anything without getting caught. The ship arrives at Skull Rock, where the fairies discover the pirates’ camp and a mysterious Pixie Dust Tree, which Zarina had grown using pink-colored pixie dust of the garden talent.