Roxas is the newest member of Organization XIII, a mysterious group who even he doesn’t know too much about. Left with no memories of who he was before joining, Roxas has nothing to go by but his given name and the number of days he’s spent in the Organization. The other members show him the ropes and teach him the basics of what his role is in the Organization’s plans, and soon, Roxas begins to take a liking to one member in particular, Axel.
The two of them get to know each other little by little each day, meeting at the Twilight Town clock tower after their missions are complete for ice cream. Though they both lack a heart, they enjoy each other’s company. Shortly after Roxas joins the Organization, a new member who hardly ever says a word joins. Roxas is curious because this new member can also wield the Keyblade, just like him.
A few days later, Axel is assigned to a new project over at a place called Castle Oblivion, as well as several other members of the Organization. Separated from his partner, Roxas is paired up with the newest member, Xion, and in time, she begins to open up to Roxas as a friend. When Axel returns from Castle Oblivion as the only survivor of a major conspiracy, he joins Roxas and Xion and the three of them become inseparable friends in no time.
But the days of meeting friends and having ice cream start to fade away when Xion is assigned to take out a mysterious impostor posing as a member of the Organization and fails. The impostor introduces himself to her as Riku, and tells Xion that her Keyblade, like herself, is a sham.
As Xion begins to question who she really is, she leaves the Organization in search of answers – answers that lead her back to Riku. Meanwhile, Namine and DiZ are hard at work reassembling Sora’s memories, which according to Namine, are beginning to affect Xion. It seems as though some of Sora’s memories escaped and made their way into Xion, and these memories start to alter the way Xion sees the Organization.
Not much longer after she leaves, Axel and Roxas are assigned to bring her back into the Organization. Roxas tries to reason with her, begging her to come back of her own free will. But faced with what she now knows about who she really is, Xion says she can’t return the way she is. Axel is forced to step in and take her by force.
It’s only a matter of time before things resume somewhat normally and the three of them are back together, having ice cream each day after their missions are complete. But part of Xion can’t help but continue to wonder who she really is, and how she is connected to this Sora that Riku has told her so much about. Xion leaves the Organization again in search of Riku to find answers, and she meets Namine, who explains to her the connection between her, Roxas, and Sora. Riku gives Xion time to make her decision about what she wants to do, but when she waits too long, Axel is forced to drag her back to the Organization again. He succeeds, but the battle drained much of his strength, and so when he returns to the castle with her, Xion overpowers him and leaves again.
Roxas, beginning to question the motives of the Organization and how they’ve been treating him and Xion, sets out to leave just as Xion did. In an effort to stop the Organization’s plans from falling apart, Saix steps in to stop Roxas from leaving, but Roxas’s strength proves to be too much. Roxas flees to Twilight Town, where he encounters Xion, who no longer looks like herself. Xion explains to Roxas that she must go be with Sora, and that she must make Roxas a part of Sora too. When she attacks, Roxas fights back and defeats her, only to forget everything about her as she fades away into nothingness. Before she disappears for good, Xion begs Roxas to free the hearts that they’ve captured and prevent Xemnas from getting hold of Kingdom Hearts.
Roxas returns to The World that Never Was to free the hearts, but he is interrupted by Riku. The two clash, and when Roxas’s power proves to be too much for Riku to overcome, he gives in to the darkness he’s been holding back in order to subdue Roxas. DiZ takes Roxas in and places him in an alternate reality until Sora is ready to awaken.