The story starts at Memory's Skyscraper, where Sora is attacking Roxas. The entire idea behind this is because Sora wants to absorb Roxas to become whole. Roxas refuses to let this happen, and he falls unconscious because he is defeated.
Roxas wakes up, finding himself inside Sora, but finds his way out, stealing half of Sora's heart in the process. He finds Axel, who is then attacked by Lea, who flees. Xigbar is then met, and Braig appears. They both die.
Sora appears, and he dies.
And then... eh, just read it...