The story covers the story of Roxas before the events of Kingdom Hearts II. On the day he is born as Sora's Nobody when Sora transforms into a Heartless in the original Kingdom Hearts, Roxas is found by Xemnas, the leader of Organization XIII, who names him its thirteenth member. Each day he is sent on missions to other worlds, either alone or accompanied by his fellow members, to destroy Heartless with the Keyblade and release captive hearts, with which the Organization can fulfill their goal of summoning Kingdom Hearts and become complete beings. Roxas is placed under the care of Axel, who he befriends and spends his spare time with at the end of each day, sitting atop the clock tower in Twilight Town, speaking what's on their minds and eating sea salt ice cream together.
Shortly after Roxas's induction, the Organization sees the arrival of a mysterious fourteenth member, Xion. Later, when Axel and several other members are assigned to Castle Oblivion (setting the stage for Chain of Memories), Roxas is paired with Xion. The two begin to bond, and the reclusive Xion begins opening up to Roxas, revealing her resemblance to Sora's friend Kairi, and her ability to wield the Keyblade. A few days later, Roxas falls into a coma for several weeks, around the same time Sora is put to sleep to regain the memories he lost in Castle Oblivion at the end of Chain of Memories. When Roxas finally awakens (and finds that all the members dispatched to Castle Oblivion, except Axel, have been eliminated), he suggests that he, Axel and Xion all spend time together, and the three become close friends. However, Roxas begins experiencing Sora's memories and grows frustrated when his questions about them go unanswered, becoming increasingly curious about why he wields the Keyblade and doubtful of the Organization's motives.
Meanwhile, Sora, who is still sleeping, is moved from Castle Oblivion to Twilight Town by DiZ and Naminé, who are overseeing the restoration of his memories. Xion also has a confrontation with Riku, who brings her identity and the authenticity of her Keyblade into question and suggests she leave the Organization to merge with her original self. Xion, however, is torn between doing and staying with Roxas and Axel.
Eventually Xion discovers that she is an imperfect replica of Sora created by Xemnas from Sora's leaking memories should Sora, who Xemnas intends to use as part of the Organization's plans, turns out to be of no use. Her resemblance to Kairi is a result of Sora's strong memories of her; however, as Naminé attempts to restore Sora's memories, they affect Xion instead to the point where she begins to physically resemble Sora. Upon learning this, Xion goes insane and leaves Organization XIII, desiring to become a true person, but also having a falling out with Roxas and Axel. Upon fully gaining Sora's appearance, Xion attempts to absorb Roxas and become whole, though this would mean the real Sora will never awaken. However, Roxas battles and defeats Xion, who reveals Xemnas's motives and intentions to him before merging with him which, in turn, halts the restoration of Sora's memories completely.
Roxas defects from Organization XIII to find himself, much to Axel's chagrin. Soon afterward, he encounters and battles Riku, who had been dispatched by DiZ to capture him so that he may merge with Sora and complete the restoration of his memories. When Riku is nearly defeated, he taps into the growing darkness in his heart, granting him the power necessary to subdue Roxas, but also giving him the appearance of Xehanort's Heartless, who resides in his heart. Riku subsequently brings the unconscious Roxas to DiZ, who digitizes and places him into a virtual Twilight Town, setting the stage for Kingdom Hearts II.
it says this on the credits:
Utada hikaru - sanctuary (after the battle)