Jiminy is looking through the 1st Journal, that went blank during CO.
In KH2, when they all woke up, Jiminy discovered the message "Thank Namine"
Jiminy finds a 2nd message in the back of the Journal that says "You must return to free them from their torment."
Jiminy shows Mickey this message, but Mickey can;'t figure out what it means.
Mickey digitzes the Journal, making a universe in the computer containing the worlds from KH1.
Data Sora, also made from the Journal, awakes to go through the Journal.
Data Sora pretty much relives KH1. A person in an Org. Cloak appears, and Sora tries to figure out who he is while he relives KH1.
Every once in a while a new message appeared in the Journal, along with a scene on the screen of Mickey's computer. 2 of these scenes are events Sora didn't experience, but Riku. The Journal is supposed to be a reflection of Sora's memories, so this is very odd, but the game never addresses it. It seems to suggest that Sora has some of Riku's memories, but we have no idea how this is possible. Probably something we'll hear about in the future. [The Zexion, Riku/Sora/Xion/Roxas scene in Days also suggests this]
Later on it's discovered that the Org. Cloaked person looks like Riku. It isn't a data Riku though, it's the Journal itself taking on the form of Riku.
Data Sora meets a Data Riku later on in Neverland. This conversation doesn't tell much, but foreshadows torment that the real Riku and Kairi (will) have.
Maleficent and Pete show up later on. They're the real ones. They had entered the data world. I'm not sure of what their motives were, but it probably wasn't important.
Maleficent destroys Data Sora's Keyblade when they battle.
Stuff happens, and irc, the Data World starts to collapse.
Data Sora goes and tries to save Mal and Pete, despite what they've done. Data Sora finally gets to them, but is too late. A Darkside Heartless destroys Mal and Pete, deleting them.
The Data World, and everything in it is deleted.
Later on, Mickey decides it's necessary to delve into the Data World once more. A new Data Sora awakes, without any memories of the previous events. Mickey meets him in Traverse Town. They wind up at Castle Oblivion.
A new Org. Cloaked figure meets Data Sora. He tells him: "You do not understand true torment"
Data Sora goes through Castle Oblivion. On each floor he goes through a Disney World, and eventually Destiny Island. After each world Data Sora visits, he forgets everything about the world, even that he went there. The further and further Data Sora goes through the castle, the sadder he gets. Yet, he knows not why he is sad.
Eventually, Data Sora and the Org. Cloaked figure speak again. The Cloaked man tells Data Sora that he just went through those worlds, and that he forgot everyone he met in those worlds.
Data Sora comes to this realization: "Even though you don't know you forgot someone, it's still sad you can't remember them." This is why he was getting Sadder and Sadder throughout the castle.
The Org. Cloaked figure is revealed to be a Data Roxas. He replies to Data Sora's realization with this: "Now you understand true torment." This hints that it's the memories of Xion that Roxas forgot are what torments Roxas.
But then during the conversation between Data Sora and Data Roxas, you see the Data Twilight Town from KH2. Data Roxas says this, "I'd like to return there."
To which Data Sora replies, "Your Summer Vacation."
And now we have Roxas with 2 torments. Memories of Xion, and his stupid Summer Vacation.
Data Sora then meets Data Namine. Data Namine tells Data Sora and Mickey a bunch of stuff. Data Namine is actually a message left behind by the real Namine, who also left behind the two messages in the Journal. This part of the game is where the events of BBS and Days are really brought into a present time problem. Namine reveals that RAX and TAV and herself are in torment. But, we already knew her torment from past games, namely CoM and KH2FM+. Sora never said "Thank You." Data Sora fulfills Sora's promise and Thanks Namine, releasing her from her torment.
Mickey returns to the real world, and the Data World is deleted. A final message appears in the Journal, "Their torment has been lessened."
Mickey writes a letter to Sora, Riku and Kairi. The letter basically just tells Sora that there are still problems, bigger and badder problems than before, and he is the only one who can fix it all.
Then you have the Re:coded secret ending wit hte conversation between Yen Sid and Mickey.
The End.
Spoiler Show
