Kingdom Hearts II begins where Kingdom Hearts: Chain of Memories and Kingdom Hearts 358/2 Days leave off. Sora and his companions have been asleep for about a year, regaining their memories. When Sora awakens, he eventually arrives in Twilight Town, the place where a mysterious boy, Roxas, lived before he suddenly left.

Gaining new clothes and powers, Sora began his journey anew, unaware of the events that have taken place in Chain of Memories. Sora continues his quest by unlocking paths to new worlds, learning of Nobodies and fighting the Heartless, as well as facing the remaining members of the mysterious Organization XIII. As the game progresses, Sora learns about Roxas and how much they have in common.

The story begins with the player in control of Roxas in Twilight Town. Roxas has dreams of Sora's adventures while increasingly mysterious activities begin taking place in Twilight Town during Roxas's 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.