Set after the events of Kingdom Hearts: Chain of Memories, Kingdom Hearts II follows Sora and company on yet another quest. Riku and King Mickey remain elusive while a powerful new enemy rises - the Nobodies, which are the remnants of the body and soul left behind when the heart is consumed by darkness (thereby creating a Heartless) and there are also those commanding the Nobodies, Organization XIII. So Sora sets out again with Donald and Goofy, in search of Riku and King Mickey, and eventually to contend with the schemes of Organization XIII.
While Sora still lies asleep in his Memory Pod, a young blond haired youth named Roxas awakens within a - unbeknownst to him - digital Twilight Town. After Roxas was brought down by Riku, Roxas was taken to this digitalized Twilight Town with false memories and a new life.
As strange things occur - white creatures attack the town, Roxas' reoccurring dreams of Sora, and the occasional visit from Axel - Roxas and his friends Olette, Pence, and Hayner spend their the last week of their Summer vacation attempting to solve these mysteries. Eventually, however, Roxas' summer vacation comes to an abrupt end after he learns of his improper existence and of Sora, whom he must return to in order for the last parts of Sora's memories to be restored and so that he may finally awaken.
With his memories fully restored - with the exception of those pertaining to Castle Oblivion - Sora emerges from his Memory Pod and is greeted by his companions Donald and Goofy. However, things are not as peaceful as they should be, despite the fact that Sora defeated Ansem Seeker of Darkness, and helped Riku and King Mickey seal the Door to Darkness, Heartless are still abound and causing havoc, and now there are the Nobodies, which are posing an even greater threat to the worlds. But none threat is greater than that of Organization XIII who Sora learns, from Master Yen Sid, must be stopped.
Every time Sora uses his keyblade to defeat an artificial Heartless, the heart that is released is collected by an ever-growing Kingdom Hearts that Organization XIII plan to use to regain that which is rightfully theirs - their hearts. Xemnas' plan is to fill the distance between him and Sora with as many artificial Heartless as possible, so that Sora will inadvertently collect hearts for their Kingdom Hearts.
So, Organization XIII members station themselves at various worlds, attempting to find powerful hearts to turn into Heartless, so that Sora will come along and collect that powerful heart for them. Sora is none the wiser as he travels from world to world in search of Riku, that he is helping Organization XIII every time he destroys a Heartless.
During Riku's fight with Roxas, Riku, near defeat, had to do that which he feared - succumb to the darkness, this would allow him to defeat Roxas, and help Sora get back his memories. When he did this, he took on the appearance of Ansem Seeker of Darkness. With this new look he took to helping Sora from afar, rather than show Sora his horrible appearance. Riku and Mickey continue to investigate Organization XIII and their plans, while Sora fights off the Heartless, and the occasional Organization member.
Mickey soon discovers some disturbing news which he reveals to Sora during a visit to Radiant Garden. Mickey finds out that Ansem Seeker of Darkness was not at all Ansem's Heartless, but the Heartless of an apprentice to Ansem named Xehanort. What is more, the leader of Organization XIII, Xemnas, is Xehanort's Nobody.
As the remaining members of Organization XIII fall, Sora's journey begins to take a close when at last he finds himself at The World That Never Was with Donald, Goofy, and Mickey. Riku's journey also brings him to this dark world where he saves Kairi and Naminé from their imprisonment.
Sora and gang are not alone in this world, however, DiZ (Darkness in Zero) - who is revealed to be the true Ansem - set up his made machine to gather data on Kingdom Hearts. The machine soon reaches critical mode and backfires, sending Ansem reeling into the Realm of Darkness.
Xemnas is finally brought down by Riku and Sora, and they find themselves stuck in the Realm of Nothingness. Sora and Riku carry on, and come upon a dark soothing shore, a shore called the Dark Meridian. Content with being stuck here, the two best friends sit down on the shore, but are soon met with a letter in a bottle that washes ashore. In the bottle lies a letter from Kairi to Sora. After reading the letter the Door to Light appears and the two friends disappear through it and are brought back home, where they are warmly greeted by Mickey, Donald, Goofy, and Kairi.
A letter in a bottle reaches Destiny Islands, one that bears King Mickey's symbol. The three friends, Sora, Riku, and Kairi, gather around and read the letter that unmistakably has news of their next adventure.
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