I apologize for the lack of understanding, but I've been gathering bits and pieces of KH:Coded and I'm trying to get the full picture.
So let's see how correct I am...
After the Disney group returns to the castle, Jiminy finds "We must return to free them from their torment." inside his journal. Mickey attempts to digitize the contents of the journal and a digital replica of Sora is created as the representation of Sora's chronicled adventures throughout KH1. So, he vanquishes the bugs that were created and the 'torment' is 'lessened.' Soon, he meets a figure in an organization robe and, after some other events, it turns out to be the journal itself, manifested into a humanoid form, taking Riku's design as a model. He explains that MDG were transported into the journal, and coincidentally, Pete and Maleficent happen to be attempting (once again) to take over Disney Castle. As this happens, they're teleported into the journal world as well. Some more events take place, and eventually Riku-Journal is captured, and brainwashed(?). Some more battles and events take place and eventually, Sora travels into a world designed to be Riku-Journal's memories, where all of his abilities are lost. He retrieves them, but Mickey reveals that unless the worlds are deleted, the bugs will never be fully destroyed (that's where it gets hazy for me). So, Sora accepts this as well as the consequences (referring to his inevitable memory loss). After this, Sora is taken out, but Pete and Maleficent don't make it. Then, a path to a new world opens in the journal, and Mickey decides to go with Data-Sora because without his memories, he wouldn't even know where he is, let alone what he should do. Sora makes it through CO, and somehow, his memories return in the process(?). Next, after beating Roxas, he meets the journal's interpretation of Naminè, who tells Mickey and D-Sora that the bugs were caused as a side-effect of the real Naminè restoring the real Sora's memories(?) (Now, it's very hazy.) In addition to this, D-Naminè reveals to Sora that the real Naminè programmed that message into the journal to reveal that three keyblade wielders (most-likely referring to VAT) are in need of the real Sora's assistance. After this, Mickey writes Sora the letter that turns up at the end of KH II.
I'm really confused about many aspects of this game. But, am I on the right track?