After a brief intro with Axel, and a cutscene involving Xion being inducted into the Org, Roxas goes on his first real missions with Marluxia, Zexion, Larxene, and Lexaeus. They teach him about the Heartless and the Keyblade, occasionally dropping hints about "Nobodies" and Kingdom Hearts itself. During all this, Axel treats him like a friend, Saix treats him coldly, Xemnas acts like he's kind in front of him but really treats him like a tool, while the rest just treat him like a child.
Eventually, the COM members called away to Castle Oblivion, and on Day 23, Axel's deployed, too. With those six mysteriously gone, Roxas goes on a few missions alone. Before long, he's paired with Xion, and they start bonding. Roxas becomes the first person Xion connects with -- the only one she really talks to, and the first one she drops her hood to.
Roxas and Xion go on a mission in Twilight Town, but encounter Darkside. Darkside knocks Roxas' keyblade out of his hand, and it lands conveniently near Xion. She picks it up, and one-shots Darkside before it crushes Roxas.
Then comes Day 27. After a mission to Agrabah with Xigbar, Roxas collapses. Before it all fades out, though, he catches a fleeting mental glimpse of Sora being sealed in his pod at the end of CoM. As Roxas sleeps, Saix and Xemnas watch over him, commenting on Namine's influence on him through Sora. Xion visits him, too, and leaves a seashell on his nightstand every day. While Roxas sleeps, we see an extended version of the Dark Beach dream from KHII.
On Day 50, he finally wakes up, only to find half the Organization still missing.
Eventually, Axel turns up again, completely out of the blue. He and Roxas go up to the clocktower to have some ice cream, but Roxas has a confession -- while Axel was away, he'd been having ice cream with someone else. Axel guesses right away that it was Xion, and Roxas says he really wants to have it together sometime, all three of them.
Back home, Saix confronts Axel one-on-one -- probably about what took him so long. Saix says he thinks Axel let Namine go, but Axel just shrugs it off. As Saix turns to leave, Axel mentions something about Zexion with a smirk.
Later, Roxas and Xion are sent to exterminate some Neo Shadows in Beasts Castle, and Xion attempts to summon her Keyblade, however, this fails, so Roxas gives her his and picks up a stick to use instead. After the boss battle, she gives the Keyblade back to Roxas, and insists that she does not need to borrow it anymore, having revealed that she can now summon the Keyblade on her own. Roxas still has his Keyblade though, so now they both have Keyblades.
Right around then, Xemnas also gathers the Organization at the Alter of Naught. He unveils Kingdom Hearts, having finally collected enough hearts to manifest in TWTNW.
One day, Xion mysteriously doesn't show up for ice cream, and the reason is because she had a run down with Riku. The full flashback is revealed when Roxas notices Xion sitting by herself on the Clock Tower.
During the flashback, she is attacked by Riku for no apparant reason. He then knocks her over, and removes her hood, and takes a peek at her face by moving his eye cover up a bit. He says "It's... It's you. Just who are you?". Then she gets annoyed when he insists that her Keyblade is fake, so she goes to attack him, but is welcomed with a punch to the stomach. Riku walks off calmly. Xion then screams very loudly.
She is awoken from the flashback by Roxas saying 'Hello? Xion?' and more Ice Cream.
