The game takes place after the events of Kingdom Hearts II and follows the story of Jiminy Cricket, King Mickey, Donald Duck and Goofy in Disney Castle. While organizing the records in Jiminy's journal from his travels with Sora and his friends, Jiminy Cricket's curiosity about the line "Thank Naminé" results in him finding a message that he did not write: "Their hurting will be mended when you return to end it." To investigate this message, King Mickey digitizes the contents of the journal and goes into the simulated world to investigate; awakening a virtual Data-Sora on the virtual Destiny Islands to carry out the contents of the journal to uncover the identity of those who are "hurting".