Kingdom Hearts II/WMG

The surviving members of Organization XIII got what they wanted.
In 358/2 Days, nine of the bosses you fight are giant Emblem Heartless. Of those nine, one was created by Pete to destroy Roxas, but the other eight are of unexplained origin. That's right...eight. As in, the same number of Organization members who made it to Kingdom Hearts II. Now stay with me here: It's mentioned on the Fridge page that when a Heartless is destroyed and then it's Nobody are destroyed, in that order, the original complete being is reborn. So what if those eight heartless Roxas was sent to kill by the Organization were the heartless of the eight surviving members? Then when those members were killed, the original beings would have been reborn, with their hearts intact. In other words, Roxas and Sora collectively gave the Organization what they wanted.
 * Eh...never mind. I just realized this theory doesn't work.
 * Why not?
 * At a guess, I'd say because Emblem Heartless are artificially created, while any living person's Heartless would be a Pureblood.
 * Well that too, but my reason was because I'd incorrectly counted the number of Organization members (Roxas excluded, since he isn't one of them when the game starts) who made it to the second game: Axel, Xemnas, Luxord, Xaldin, Demyx, Xigbar, Saix. That's only seven Organization members in KH2 and eight Emblems killed by Roxas in Days. (Again, not counting the one Pete sent to kill him.) In order for this theory to hold true, we would have to except that the Organization just sent Roxas after an extra Heartless for no particular reason.

Sora's adventure is shattering his mind.
People complain that KH 2 Sora doesn't feel like the regular Sora at all and is just a stereotype of a 90s teenager. This was an intentional ploy by the writers to show how Sora's journey has left him so shattered that he's forced to develop alternate personalities to handle the various turmoils in his life. That's why he can go from "Let's star in a musical~" to "RAWR KILL THE ORGANIZATION" at the drop of a hat.

Proof that Sora would have some trauma:

1. His world was destroyed in front of his eyes.

2. Forced to kill monsters from "the black lagoon" without any experienced adults helping him (consistently). Seriously, why'd Leon and Co. let those three go alone? They had no way of knowing whether they'd get help from others on different worlds.

3. Being forced to kill humans/humanoid people. (Shan-Yu, Organization XIII, Ansem, etc.)

4. Suicide by Keyblade.

5. Literally being mind-****ed by Namine.

6. Having more people come out of him than Octomom. (Roxas, Xion, Namine, etc.)

7. Having to (possibly) assimilate some of Ven's traits as a child might've led to a suppression of his own personality. (This one is more speculation than the others.)

The Scar that climbed up the mountain after being killed was his Nobody
This would be why he kept his appearance and gained elemental power (darkness, apparently). Pete said heartless because he is an idiot.

Why Sora's Reactions to Kairi and Riku Are Different

 * Yes, I'm talking about THAT scene.You see, Sora, having a fairly large crush on Kairi, always imagined the two of them together, but when he's actually with Kairi, he Cannot Spit It Out. Boys, how many times have you approached the gal of your dreams only to act like a total idiot and either fumble with words, or act completely uninterested? So he does the only thing he can think of without looking stupid; just hug her back.
 * Meanwhile with Riku, Sora's letting out all of the worry he's had over Riku being consumed by the Darkness. Wouldn't you be worried if your best friend was turning evil? or had a pretty good chance of being lost to the Darkness forever? Sora's just relieved to see he's okay, and also a little pissed that Riku didn't tell him he was in the first place. He isn't gay, just extremely worried for his friends, which fits with his personality perfectly.
 * It is also worth mentioning that despite being separated, Kairi expent that year safe at their homeworld. Riku, in the other hand, was thought to be lost forever, and while Sora knew Riku was back for a while thanks to Mickey, finally meeting with Riku cracked him, because he finally made sure his best friend was alive.

Setzer was deliberately made to be Out of Character.
Similar to how there are other blips in reality during Roxas' days in the prologue, Setzer acting drastically different than his usual self (such as stooping to bribery) is a sign of the unreality that Roxas is inhabiting.