Starting a Journey may not be so hard

A year has passed in Kingdom Hearts II following the events of Kingdom Hearts I and Chain of Memories. Sora, Donald and Goofy have been in suspended animation. Sora, Donald, and Goofy wake up in the real Twilight Town after his Nobody, Roxas, is returned to him. There, they meet King Mickey and Yen Sid, who once again send them on another journey. Their goal is to find Riku and figure out the plans of Organization XIII, who control the Nobodies who are empty shells left over when a person with a strong heart is transformed into a Heartless. Afterward, Maleficent is resurrected and joins with Pete to continue her quest for power.

Sora travels to many Disney-themed worlds, old and new, and resolves several problems caused by Organization XIII, the Heartless, and various Disney villains. During a visit to Hollow Bastion, they again meet King Mickey, who reveals the Heartless "Ansem" they defeated to actually be an imposter named Xehanort, whose Nobody, Xemnas, is the leader of the Organization. Organization XIII's plan is also finally revealed: they seek the power of Kingdom Hearts to regain their lost hearts. Sora revisits the worlds to solve lingering problems and new complications, while seeking a path to Organization XIII's base of operations. Throughout his endeavors, Sora is secretly aided by a mysterious hooded figure whom Sora believes to be Riku.

Following a lead, Sora, Donald, and Goofy enter a passageway through Twilight Town. After fighting and joining Axel, Axel decides to sacrifices himself to create a passageway to the World That Never Was, the headquarters of Organization XIII. Sora finds Kairi and Riku. King Mickey encounters DiZ, who reveals himself to be the true Ansem, Xehanort's mentor. Ansem uses a device that dissipates some of Kingdom Hearts' power, but a system overload causes the device to self-destruct, both engulfing Ansem and miraculously returning Riku to his original form. At the top of the Castle That Never Was, Sora and company battle Xemnas, who uses what remains of Kingdom Hearts to power his multiple forms.

After Sora and Riku destroy Xemnas, the two are reunited with their friends at their home, Destiny Islands. A post-credits scene shows Sora, Kairi and Riku read a letter from Mickey, which is hidden from the player.