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At the beginning of the Kingdom Hearts Birth by Sleep, a young man stares at the sunset and states that the world was too small. Many years later, he returns, intending to leave his seemingly dying, comatose apprentice, Ventus, at the islands for his final days. However, Ventus's broken heart connects with that of the newborn Sora, and he revives, summoning his Keyblade. Seeing further use in the boy, Xehanort immediately takes him to Master Eraqus at the Land of Departure.
Terra is the first of the three Keyblade wielders to visit Destiny Islands. There, he watches a young Sora and Riku practice sword-fighting. After asking Riku why he wants to leave the islands, Riku explains that a man once left the islands to visit other worlds, and that he wants to do the same. Terra sees a vision of the man, then sees what Riku will become, convincing him to choose Riku as his successor so that one day he may wield the Keyblade.
Ventus later arrives on the island, where he finds Vanitas and learns the truth about his past, but never encounters Sora or Riku.
Aqua is the last to arrive on the island. After recognizing that Sora and Riku's friendship is identical to the bond between Ventus and Terra, she decides to choose Sora as her successor, but when she discovers that Terra has already chosen Riku, she changes her mind, not wanting to force the friends to fight. Instead, she asks Sora to save Riku if he were to ever fall into darkness.
On a night after Master Xehanort is defeated, Sora and Riku watch the stars on a beach facing the Small Island. As they prepare to depart home, Sora suddenly feels Ventus's sadness connecting with his heart. Riku advises him to try and reach out to that sad heart, and as Sora connects to Ventus's heart he enters his first Dive to the Heart. He joins his heart with Ventus's, hoping to make it happy again, then tells Riku that he was right as they go back to watching the stars.
In a prophetic dream, Sora is swallowed by the tide while trying to save Riku and is transported to another world.
When Sora awakens from his Dive to the Heart, he meets with his friends Kairi and Riku. The three plan on building a raft and to set sail across the sea to find other worlds away from the island. Destiny Islands is a small world, which often leads to the boredom of its inhabitants, especially Riku, who desires to leave the islands and see the other worlds out there. Tidus once said that once you sail a certain distance from the islands, you simply can't go any further, but the other islanders believe he merely turned back and made up the story.
While gathering materials for the journey, Sora climbs into the Secret Place - a tiny cave on the island where the children scratch drawings onto rocks - and met a figure in a strange cloak who told him cryptic messages about the time to come. Sora's confusion lasts long into the night. Resting up in his bedroom, he sees a dangerous storm approaching, and hurries off the island to save the raft.
Upon arriving on the second island, Sora discovers his friends came too, but only finds Riku, who confuses him further by telling him to accept the darkness, after which, Riku disappears. He then finds an apparently-ill Kairi in the Secret Place. The two disappear in the growing darkness, but Sora returns as the Islands slowly crumble into darkness with the Keyblade in hand. He fights with the Darkside boss, but fails to save his home, and is whisked away on his journey to Traverse Town.
As his first journey ends, Sora and Kairi meet up on the shores of the reforming islands. Sora, knowing that his job is not finished and that he must still save Riku and King Mickey from the Realm of Darkness, leaves Kairi in the safety of her hometown and promises to return to her as soon as Riku and King Mickey are found.
During the credits, you see Tidus, Selphie, and Wakka running on the beach in a similar way to Riku, Sora and Kairi do earlier in the game.
After the Riku Replica is defeated on the 11th floor of Castle Oblivion, he drops his Wayfinder charm, which is revealed to be the World Card for Destiny Islands. Sora rushes to use it in order to get to Naminé, but when Goofy and Donald urge him to be cautious, he angrily rebukes them and goes through the memory world alone. Naminé manipulates his memories to make Sora believe she also lived on the Destiny Islands, and Sora is urged by his memories to rescue her. However, after he defeats a memory Darkside, Naminé appears and reveals the truth about Kairi, herself, and what she has been doing to Sora.
After Riku defeats Lexaeus, Zexion appears with a world card and entices Riku to enter his own version of Destiny Islands. Unlike Sora, Riku finds no one on the islands, except a memory of his Darkside, the one who devoured the islands. After defeating the monster, he sees "Sora", who is in actuality Zexion in disguise. "Sora" accuses him of being a monster of darkness, and attacks him with light. In the light, Riku considers giving up, but Naminé (disguised as Kairi) speaks to his heart and urges him to use both his light and his darkness, which are invincible together. Riku sees through Zexion's disguise and attacks, forcing Zexion to flee.
During Sora's sleep, the residents of the Islands forget all about Sora, due to Naminé breaking the chains of his memories. Kairi, however, being so close to Sora, still retains vague memories of the boy, and begins to remember before anyone else. She sends a message in a bottle across the sea, hoping to find Sora.
Finally, after Xemnas is defeated, all the characters meet up on the Islands for one last time. King Mickey, Jiminy, Donald, Pluto, and Goofy return to Disney Castle, and leave the others on Destiny Islands. But, in an extra video after the credits, it is seen that Mickey has sent a letter in bottle back to the islands for Sora, Riku, and Kairi.
Roxas, Axel, and Xion visit the island in separate occasions. During Xion's nightmare, she transforms into Roxas, Riku, and Sora while listening to the speech that Zexion gave Riku near the bent palm tree.
After King Mickey and Jiminy discover a message in Jiminy's Journal, they create a data version of Sora. After Sora exits his Awakening, he finds out that the island is covered with Bug Block Corruption which the Data-Sora must delete. Afterward, he encounters Jiminy's Journal wearing the Black Cloak. He then finds the Data Keyhole behind the waterfall of Destiny Islands. After he opens it he fights Darkside, the island's source of Bug Block corruption. Then the data island is destroyed, just as it was in the first game. The scene then shifts to Disney Castle where a cutscene is played. It shows Ansem, Seeker of Darkness appearing and opening the Corridor of Darkness for Riku to step in. The real Destiny Islands appear in the game's final scene, where Mickey sends Sora the bottled letter (the same one from Kingdom Hearts II), which Sora reads with Riku and Kairi.
- Destiny Island is an anagram for "It's Disney Land".
- In Kingdom Hearts II, the world is called Destiny Island.