After the events of KINGDOM HEARTS II, Jiminy Cricket is reviewing his journals from the previous two adventures. Perplexed by the mysterious line left in the journal from their first journey (Thank Naminé), Jiminy begins to sift through its pages. He stumbles across another message written into the journal – a message he didn’t remember writing.
He brings the journal to King Mickey, who decides that the best way to determine the origin of this mysterious message is to scan the journal into a computer and explore the data. King Mickey, Donald, Goofy, and Jiminy communicate with a Data-version of Sora already within the journal to re-explore the worlds visited in their first journey.
Thus, Data-Sora’s adventure begins. He sets out to fix the corrupted data within the journal and restore the data to its original state. With each new world Data-Sora fixes, new messages are revealed from deep within the journal of events that Donald, Goofy, and Jiminy don’t remember.
As Data-Sora makes his way further into the corrupted journal, he suddenly finds his way into the library room where King Mickey, Donald, Goofy, and Jiminy had been monitoring him from the outside world. It is at this point that a mysterious hooded figure appears in the library and reveals himself to be a physical representation of the journal in the form of Riku. Riku tells them that the mysterious message written in the journal was not his doing, and that he has brought King Mickey, Donald, Goofy, and Jiminy into the Datascape to help unravel the rest of the mystery.
Data-Sora agrees to go back into the worlds, defeating the bugs and restoring the corrupted data. He eventually discovers that Maleficent and Pete have found their way from the real world into the Datascape, and are attempting to take over the data world. They claim Riku and corrupt him with bugs, brainwashing him to serve them. Data-Sora fights with Riku to free him from the bugs, only to be sucked inside his data. Data-Sora must now work to fix the corrupted data within Riku in order to save the journal.
Upon fixing Riku, Data-Sora’s memories are erased and King Mickey, Donald, Goofy, and Jiminy are transported back to the real world, along with Maleficent and Pete. Riku contacts King Mickey and the others through the computer, telling them that he has discovered a hidden world in the journal’s memory – a world that could possibly hold the key to uncovering the truth behind the mysterious messages in the journal.
King Mickey re-enters the Datascape and contacts Data-Sora, whose memories of his past adventure in the journal have been wiped clean, and asks him to explore this new world in the hopes of learning the secret of the message. It is upon entering that world that Data-Sora and King Mickey discover a much bigger truth than either of them were anticipating, and it falls on King Mickey to notify the Sora in the real world of the journey ahead of him. King Mickey immediately gets to work writing a message in a bottle — the same message that Kairi brings to Sora in the epilogue of KINGDOM HEARTS II.