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Kingdom Hearts II begins where Kingdom Hearts: Chain of Memories left off.

Roxas has recurring dreams of Sora's adventures and increasingly mysterious activity is taking place in Twilight Town during Roxas' summer vacation. After obtaining the Keyblade to defend himself from the Nobodies, Roxas comes in contact with a young man in black named Axel. Axel appears to know Roxas, though Roxas has no recollection of him.

Roxas eventually makes his way into an abandoned mansion where a girl named Naminé informs him that he is a Nobody, although he did not quite know what a Nobody was at that time. A mysterious, red-cloaked man by the name of DiZ also briefly appears. Then Roxas discovers Sora, Donald, and Goofy sleeping in the hidden basement of the mansion. Roxas seems to disappear at this point as Sora, Donald, and Goofy awake from their year-long slumber. Jiminy Cricket, who had previously chronicled the trio's adventures, finds that his journal is now completely blank, save for the note: "Thank Naminé" (which was written by Jiminy himself during Chain of Memories).

After speaking with Yen Sid, the party is informed that they must once again visit many worlds to protect them from both the Heartless and the Nobodies in an attempt to stop Organization XIII.

After journeying to old worlds and some new ones, Sora and the others must return to Hollow Bastion, where a massive army of Heartless are attacking the restored town. On the way to fight, the Final Fantasy characters aid the party in battle, and on one vast battlefield, Sora alone defeats 1000 Heartless.

Finally, after revisits to the world, and defeating most of the remaining members of the Organization, their ultimate goal is revealed; They plan to create another Kingdom Hearts, a doorway to the heart of all worlds, with the hearts of all the Heartless Sora has defeated, and thus, being Nobodies, get their hearts back. Sora goes to The World That Never Was to settle the score with the Organization leader Xemnas, who is really the nobody of Xehanort, an apprentice to the great scientist Ansem the Wise. The Ansem the party defeated in the original Kingdom Hearts was really Xehanort's Heartless.

In the huge Nobody Castle, Sora finally meets Riku and Kairi again, and although Riku looks like Xehanort's Heartless because he had to give in to the Darkness, he regains his original shape when a machine to decode hearts, created by DiZ (Who is revealed to be the real Ansem the Wise) explodes and kills Ansem. Ansem the Wise wanted to make amends for first researching the Darkness of Hearts. Sora learns the truth about Roxas as well; he and Naminé are Sora and Kairi's nobodies, created when they lost their hearts in Kingdom Hearts.

In the end, (after defeating Xigbar, Luxord and Saix) only Xemnas was left of the original 13 members. Sora fought and defeated him, and the new Kingdom Hearts was closed. Sora and the others were returned to the Destiny Islands, and although Sora has to say goodbye to Donald and Goofy, he knows in his heart that true friends are never gone. But he might meet them again, since Sora, Riku, and Kairi receive a letter from King Mickey after the credits.