Okay so I recently finished Terra's story on BBS and watched the endings for Aqua and Ventus and now I am like... huh? about the whole thing. Here is what I think I understand...
Terra got body snatched by Xehanhort, but is mind and/or heart remained behind in his armor which is the armor you fight in KH2FM, so now Xehanort/Ansem/Xemnas/Terra'sbody gives up on the X-blade in order to pursue the Kingdom Hearts...
Aqua got her ass trapped in the Kingdom Hearts somehow, I remember Riku was there once but he got out but I don't remember how he did it (been a while since I played KH1+2). I know Aqua wasn't there during Riku's visit, or at least he didn't see her so maybe she is out somewhere...
(This is where I get really confused)
The whole Ventus/Vanitas/Roxas/Sora thing. From what I gather Vanitas was created from the darkness that was ripped out of Ventus' heart. During the final battles of BBS Ventus and Vanitas get merged, but since Sora's heart is in there I would assume that is why the Ven/Vanitas looks like Sora. After the fight or during the fight, in order to protect Ventus' heart Sora takes Ventus' heart into his own for the time being, leaving Ventus as a heartless sleepy head in the castle of oblivion. Later on when Sora becomes a heartless he actually had two hearts in his body, one being Ventus' heart. I think that this is why Sora is not lost to the heartless and also why "Sora's" nobody aka Roxas, looks like Ventus and not like Sora (I am saying here that I believe that Roxas is actually Ventus' nobody and not Sora's, and that Sora only lost the part of his heart that was used to fix Ventus' hencewhy he was able to continue fighting on as a heartless, because he actually still had most of his own heart).
At least that is what I think or understand so far.
And Axel is SOOOOOOOOOOOOO SEXY.