Released in December of 2004, Kingdom Hearts: Chain of Memories (only available for the GBA/SP/DS) is the story of what happens to Sora and Riku in the time period between Kingdom Hearts/Kingdom Hearts: Final Mix and Kingdom Hearts II. Both Sora and Riku are trapped inside Castle Oblivion where, to learn the truth, they must first forget. Castle Oblivion's individual floors reflect different portions of the memory belonging to the hero going through them. Sora has to go through the main floors, searching for someone dear to him, while Riku is stuck in the basement floors, trying to find out whether it is true that the only thing left for him in his soul and in this world is the darkness he gave himself up to and later rejected in Kingdom Hearts.

The mysterious Organization, made up of the black-hooded Nobodies (of which one of the final bosses in Kingdom Hearts (Final Mix) is an example of), make their true debut here. All of the members of the Organization are incredibly powerful... so who are they, and what do they want with our heroes?