A week after Roxas joins Organization XIII, Xemnas introduces Xion to the other members. After looking at the other members, she smiles up at Roxas, puzzling him. As Roxas departs for his first training mission, he spots Xion shy
ly watching him nearby, and Saïx formally introduces her to Axel and Roxas.
On the day Axel is sent to Castle Oblivion, Xemnas entrusts Roxas with the task of looking after Xion, who quickly bonds with him. She reveals her ability to wield the Keyblade to him and looks after him when he falls into a coma for several weeks in conjunction to Sora being put to sleep to regain his memories. After discovering that Sora and Riku had slain all of the Organization members (except Axel) that were in Castle Oblivion at the time, Roxas, Axel, and Xion all begin spending more time together as per Roxas's suggestion and become fast friends, such as enjoying sea-salt ice cream together. After Xion asks Axel to be her friend, he accepts, and he stops seeing her as a hooded doll, and begins seeing her as the black-haired girl that Roxas sees.
However, a series of events begin to split the trio apart: while DiZ and Naminé oversee the restoration of the sleeping Sora's memories (moving him from Castle Oblivion to Twilight Town), Roxas begins to experience the process for himself, and begins to ponder over how he is able to wield the Keyblade and doubt the Organization's motives; Axel is reprimanded by their superiors for placing his friendship with Roxas and Xion before the Organization's goals; and Xion is thrown into disarray after a confrontation with Riku, who questions who she is and why she wields the Keyblade, causing her to become torn between staying with her friends and leaving the Organization to merge with her true self as Riku suggests.
Xion travels with Riku for several days before being captured by Axel and brought back into the Organization. However, Naminé's attempts to restore Sora's memories are soon halted when Xion starts absorbing them faster, causing Roxas to weaken as she becomes stronger, as Xemnas intended. Eventually, after being tricked into fighting Roxas by Saïx, Xion decides to accept Riku's advice and leaves the Organization.
After her departure, Xion comes into contact with Naminé in Twilight Town's Old Mansion, questioning her own existence and the fate that will soon befall Roxas. She discovers that she is not a Nobody, but an imperfect Replica of Roxas. Naminé also reveals that as a memory being, once Xion returns to Sora, everyone's memories of her will inevitably be forgotten. Furthermore, Naminé's attempts to restore Sora's memories not only affect Roxas, but Xion as well, stating why they both keep having memory relapses. Xion accepts the facts, and decides to go back into Sora. Before she does, though, DiZ barges in with the news that an Organization member has followed her, in which Xion says she will take care of it, despite Naminé's protests, and heads out of the mansion.
It is Axel who has arrived, having finally tracked Xion down. Not only is Axel curious of Xion's motives, he is also given specific orders to capture her again, which would possibly convince Roxas to return to the Organization. Xion refuses, leaving Axel no choice but to accomplish his mission with brute force, leading to a heated battle. Having defeated Xion, Axel brings her back to The World That Never Was, but soon faints from fatigue. Xemnas then steps out from the shadows and carries the unconscious girl away to reprogram her to use the devices he had planted throughout the worlds.
Soon afterward, Roxas finds Xion at the Twilight Town train station, and after she reveals her altered, Sora-like form to him, she explains that she has been compelled by Xemnas to absorb Roxas and become a "full" Sora, which would in turn prevent the real Sora from ever waking. It is explained in her secret reports that this is somewhat of a ruse—she knows that Roxas will disappear if she continues to exist, so she plans to force Roxas to absorb her, saving himself and thwarting Xemnas's plan. She then transforms into a monstrous version of Sora using Xemnas's devices, and attacks.
During the battle, Roxas and Xion are transported to Wonderland, Halloween Town, and Agrabah, before returning to Twilight Town. In each world, Xion absorbs power from the "devices" that were placed there, which contain memories of Sora's battles in each world. After a long and grueling battle, Roxas manages to defeat her, while she regains her original appearance in his view.
When done, he doesn't seem to recall who she is, though she assures him that he'll be better off now. Cradling her in his arms, Roxas shares an emotional conversation with her, during which she explains to him that she had no regrets for meeting him or Axel, reveals the true colors of the Organization to him, and pleads with him not to let Xemnas win before dying peacefully in his arms. Saddened, Roxas suddenly remembers her name and holds Xion's hand as her body crystallizes and disintegrates into nothingness, leaving behind nothing but a single Thalassa Shell.
Though Naminé states that everyone's memories of Xion will vanish when she dies, Roxas, Axel, Riku, Xemnas, and Saïx manage to retain some memories of her into the next day. By then, Roxas has returned to the World That Never Was in order to set Kingdom Hearts free, which he hopes will reunite him with Xion. However, he is being stalked by a swarm of Neoshadow Heartless, as well as a determined Riku, who has arrived to capture Roxas to finish Sora's memory restoration. Riku looks down upon the Nobody, before Roxas starts his path up the skyscraper.
Through him, Xion is able to throw the Oblivion Keyblade to Riku in order to tell him to stop Roxas before he can reach Xemnas, because she believes Roxas is not strong enough to face him yet. In turn, touching the Oblivion causes Riku to recall flashbacks of the time he spent together with Xion, putting him in shock for a moment. The flashbacks then reoccur when he reaches the ground to face the Neoshadows, but this time turn blurred and grainier as they continue, until only film static remains, most likely meaning their total withdrawal from Riku's memories.
When Roxas and Riku finish eradicating the Heartless, they turn on each other for a battle. By this time, it is a struggle for Roxas to even remember Xion's name, and all he knows about her is that he wants her back. While Roxas is able to knock Riku down first, Xion then somehow telepathically projects her words to Riku, to stop Roxas at any cost, and so he does once he removes his blindfold and transforms into Riku-Ansem.
Unconscious, Roxas hears Xion talking to him through his mind, telling him not to be sad, as she has become one with him and Sora, and that soon Roxas will also join them. Despite the fact that memories of Xion have been forgotten by everyone, she tells him that she still has her own memories, so she doesn't mind that he has forgotten her, as she won't forget him or Axel. As Riku knocks him out, Roxas's last memories of Xion fade away.
Xion appears very briefly in the opening for Re:coded, where various clips from the series flashes by, Xion's death being one of them. After Aqua speaks with Ansem the Wise about Sora, Xion is sitting atop the Twilight Town clock tower and eating sea-salt ice cream with Roxas and Axel. Then, Xion and Roxas say Sora's name while watching the sunset together.
Xion appears to Sora in the World That Never Was. Sora takes a grip of Naminé's wrist, but then Naminé turns into Xion. Sora then sheds a tear and wonders who the girl is. Xion then pulls away from Sora and runs away from him.
Xion later appears on Destiny Islands inside Sora's heart. She is sitting on the Paopu Tree and Riku initially mistakes her to be Sora. Xion watches the sunset and asks Riku, "Riku, what do you wish for?", Riku can then choose from three options like Sora did in the original Kingdom Hearts. Xion disappears after Riku gives her an answer.