It's twilight on Destiny Islands, and Xehanort, a silver-haired youth, watches over the sunset. He muses that this world is just too small.
Decades later, Xehanort returns to the islands as an elderly man carrying a blond-haired boy in a white bundle. Xehanort intends for the boy to live out his final moments. Meanwhile, the boy's heart comes in contact with that of a newborn, who senses that his heart is broken and offers to bond with it. As the two accept, back in the waking world, the boy summons a Keyblade, much to Xehanort's surprise.
Four years later, the boy, a Keyblade apprentice named Ventus (Ven for short), awakens to a meteor shower. He rushes out of his room to a cliff on the side, doing some training in the process, but nods to sleep shortly after. However, he is roused by his friends Aqua and Terra, fellow Keyblade apprentices who are about to have their Mark of Mastery exam the next day. After a brief sparring match, Aqua offers her friends Wayfinders, good-luck charms fashioned after paopu fruits from the Destiny Islands with magic imbued.
Meanwhile at the Mysterious Tower, King Mickey rides on a book over waves of water, but is sucked down a whirlpool. He reappears in the office of his master Yen Sid, who feels that something horrible is about to transpire.
The next day is the day of the exam. As Ven watches from the sidelines, their master Eraqus, joined by his fellow master Xehanort, commences Terra and Aqua's exam, which consists of challenging them with orbs of light. Xehanort slyly imbues the orbs with darkness, forcing Ven to join in, but the exam comes to pass. Up next is a duel between Aqua and Terra. As they fight, Terra briefly taps into the darkness, which results in him failing the exam while Aqua passes.
Master Xehanort leaves the room and enters a secret corridor where his apprentice Vanitas waits. Vanitas believes that Ventus is too weak and needs incentive to leave the Land of Departure.
Disappointed in himself, Terra sits outside, lamenting his failure. Xehanort steps outside and tells Terra that darkness, despite Eraqus's teachings, cannot be destroyed, only channeled, before leaving.
Eraqus soon calls an emergency meeting with Aqua and Terra. The two apprentices are assigned to venture out into the worlds to subdue the Unversed, negative emotions taken form as monsters, and to search for Master Xehanort. Terra takes it as a chance to prove himself worthy of the Mark of Mastery.
Meanwhile, in his room, Ventus is confronted by Vanitas, who warns Ven to hurry lest Terra will be gone forever. Though Ven asserts that Terra is his friend, Vanitas mocks him.
- Vanitas: Oh, grow up. Is that what you call friendship? You'll never know the truth unless you go out and look for it yourself. Come on, what could you possibly know when you're stuck here, looking at nothing but what's in your tiny world?
As Terra prepares to leave on his mission, Ven catches up to him and attempts to warn him, but Terra soon leaves, forcing Ven to pursue Terra. Eraqus, shocked at Ven's departure, orders Aqua to follow Ven and keep an eye on Terra.
And so, the three Keyblade apprentices set off on their own quests...