When Axel is sent to Castle Oblivion, Xemnas entrusts Roxas to look after Xion, who quickly bonds with him. She reveals her ability to wield the Keyblade to him, and looks after him after he falls into a coma for several weeks in conjunction to Sora being put to sleep to regain his memories. After discovering that all Organization members in Castle Oblivion except Axel have been slain by Sora and Riku, Roxas, Axel, and Xion all begin spending more time together as per Roxas's suggestion and become fast friends. It is possible that she may have the same abilities to control the Samurai Nobodies.
Xion confronts Roxas at the Twilight Town train station, and after revealing her altered form to him, transforms into an armored creature and attacks him in The bizzare room of Wonderland, Oogie's manor's ruins and the lamp chamber in the Cave Of Wonders where you fight Jafar in the first game, planning to kill and absorb Roxas in a delusional attempt to become a real person, uncaring that this would prevent the real Sora from ever awakening. After a grueling battle, Roxas defeats the deranged clone of his former self, who regains both her sanity and her original appearance. Cradling Xion in his arms, Roxas shares an emotional conversation with her, and she reveals the true colors of the Organization to him before dying peacefully in his arms. Emotionally shattered, Roxas absorbs Xion's degenerating body, granting him the use of her Keyblade (allowing him to dual-wield both his and hers as well) in addition to inadvertently bringing the restoration of Sora's memories to a complete stop.
It is Xion's death that compels Roxas to depart the Organization to find himself.