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Perhaps the Secret Reports (accessible end-game) would enlighten you as to her motives?
Basically, she spent the first half of the game uncovering her identity and purpose in the Org, hence her initial defection, and the second half mulling over the ultimatum (return to Sora) Riku had given her. (Riku probably also disclosed DiZ's assumptions of Xemnas' true goal to her when she was running around with him). Upon learning of her parasitical relationship with Roxas (what with her draining his power) and the Org's intention to eliminate either him or her, she decided that sacrificing herself (and having Roxas survive) was best, prompting her second defection.
LOL....haha relax we know we know....Xion is the shame of the game xDTHEN SHE HAS THE NERVE TO MESS WITH DEEP DIVE! Rape my childhood will you!? Are you telling me that Roxas didn't pass Riku the keyblade in order to fight with him, but because Xion passed it to Riku?! And then you wanna tell me that Riku fought Roxas because Xion begged him to!? What the flying eff?! I can't believe this. I really did just skip the scene. I saw it again in the theater mode. I couldn't believe it. And when she died, yeah I was sad. So sad I saw the clip again in theater mode, but I muted it cuz I was on a bus...guess what. I didn't feel a thing. I put my headphones...