The story of Kingdom Hearts: Re:Coded can be a complicated one to follow. After Sora’s latest adventure in defeating the members of Organization XIII and returning to Destiny Islands, 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 Namine), 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 determines that the best way to determine the origin of this mysterious message is to scan the journal into a computer and explore the data in search of the anomaly that led to this message. King Mickey, Donald, Goofy, and Jiminy communicate with the Sora already within the data 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. In the process, with each new world Data-Sora fixes, a new message is revealed from deep within the journal of events that Donald, Goofy, and Jiminy don’t remember from their journey.

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 reveals that the mysterious message written in the journal was not his doing, and that there is more to uncover.

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 dataspace, and are attempting to take over the data world. They claim Riku and infest him with bugs, brainwashing him to serve them. Data-Sora fights with Riku to free him from the bugs, only to be sucked into 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 message written 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.