I have a theory.
It's about Loki.
In the Thor movie, his eyes are green. But in the Avengers movie, his eyes are blue.
WHY?
Some people said it was just because the editors didn't want to change his eyes again, or that they didn't want to spend money on contact lenses, since Tom's eyes are blue.
But I think there's something else.
In the Thor movie, Loki acts very different than how he acts in The Avengers. In Thor, he is sad, angry, and rejected, and he tried to gain respect from his father.
In The Avengers, he is angry and just wants to take over a world because A; He feels he's above them, and B; He wants to release his anger for what his father did to him. Very different personalities.
But what happened on that fall off the bridge?
I think the Alien bad guys found him floating through space, and somehow took over his mind to make him want to take over earth.
But why do I think this?
When Loki takes over the minds of innocent people, he taps the sceptre to the victim's chest, and their eyes turn blue.
I believe that happened to Loki as well.
Loki was brainwashed, and could not control his actions.