Nobodies-empty shells created when a person's heart is lost to darkness. The Nobody Roxas, created when Sora released his heart to free Kairi's and who knows nothing of his past, joins the mysterious Organization XIII soon after his birth. With the help of Axel, another member of the organization, and the mysterious Number XIV, who is also missing her memories, Roxas slowly begins to learn what it takes to be a part of Organization XIII...and what it means to have a heart.

When Xion loses her Keyblade, it's Roxas' job to make sure no one finds out. As long as the two can go on missions together, no one will know that it's Roxas collecting all the hearts. But will Demyx blow their little secret? And when the Organization issues an order to Xion to capture an outsider masquerading as one of its members, who will come out on top in the ensuing battle?!

Xion, having failed her last mission, is left unconscious and out of commission. Unfortunately, Roxas doesn't have time to worry about his friend because he's been ordered to go to Wonderland with Organization XIII's No. 10-the Gambler of Fate, Luxord. Can Roxas keep up with the old man's games?!

Left alone to ponder the purpose of her existence and desperate for answers, Xion journeys alone to find out who—or what—she really is. But little do she, Roxas, and Axel know that her quest will lead to the close of one tale and the continuation of another...

With Xion back in the Organization, she and Roxas can finally work together again. But strangely, Roxas is getting weaker and weaker, while Xion is getting inexplicably stronger. Meanwhile, the leaders of Organization XIII decide that they only need one Keyblade wielder. What fate lies in store for Roxas, Xion, and Axel?!