The story is pretty simple: bad guys from distant planets taking over the earth; superheroes fighting back. In this case, it's Loki who's the baddie, the trickster god from norse myth, with lots of aliens. But this is a wonderfully atypical entry in this genre. The basic dichotomy in the movie - the dividing line between the good guys and baddies - isn't, strictly, moral legitimacy vs. moral evil. Of course, the bad guys are wrong to invade and subjugate the earth; but the contrast between good and bad which the movie focuses on is the level of and capacity for self-doubt. The heroes are well aware that they can cause as much damage as the bad guys: at one point, the Hulk character (before transforming) says, "We're not a team. We're a ticking time bomb."
Loki is completely opposite in this respect. Some villians are interesting because you can half-sympathize with them, or sort of understand their motives; Loki, on the other hand, has only the very slimmest justification for his desire to enslave the human race. Even one of his alien generals tells him that he's "filled with childish need." He wanted his father's throne, even though he proved himself unworthy of it. Both his brother (Thor) and father (Odin) reach out to him, but Loki rejects them, nurses his self-pity and sense of being wronged, and assembles an alien army to conquer the earth as a consolation prize for himself. His only justification is to salve his wounded pride. Loki doesn't weigh this against how much damage he might cause; it never even occurs to him to ask this question.
There are actually four distinct groups of characters: the avengers, Loki and the bad guys, Nick Fury, who assembles the avengers, and an undefined group of humans to whom Fury answers. Again, the capacity for self-doubt is parsed with regard to each group: the avengers are as suspicious of Nick Fury as they are of themselves. Fury himself doesn't seem overly plagued by much doubt, but when his superiors make a decision which makes a certain kind of sense in abstract--they sacrifice thousands of lives to save the planet--Fury deliberately ignores them. (I find him most likeable when he does this). Toward the end of the movie, Fury's superiors don't seem morally distinguishable from the invading aliens.
Self-doubt isn't the main theme of the movie; human freedom from outside interference is. (Loki gives a number of speeches in which he tells humans it's unbecoming for them to be free: slavery fits us much better. In his eyes, we're cattle.) And what I'm talking about sure isn't the only overlap with grace in the NT (it's hardly surprising when a certain superhero lays down his life to save the others). Nevertheless, it's striking how a main ingredient of heroism in this movie is not power (almost everyone in the movie is powerful), but the capacity to realize that I might unintentionally cause as much damage or more as a bad guy intends to.
And by "I," I mean you. Reading this. Yeah, you. Don't look around like I'm talking to someone else. I don't care if you're a Christian or not, liberal or conservative, Calvinist or Wesleyian, Prodestant or Catholic. However you self-identify, the finger is pointing at you. You can cause as much damage as the bad guys, without ever meaning to, all the while thinking you're a decent chap who's in the right morally.
The gospel requires us to take a stand against ourselves before God; to agree with God's condemnation of our sin and our righteousness in the cross; to admit that, on our own, we multiply sin and pain, whether we mean well or ill. Bowing before the cross changes your relationship to your past and your future from self-justification to at least self-suspicion, if not self-condemnation. Forever after, you have to keep wondering, Am I the bad guy here? ("Meet it is that I set it down: That one may smile, and smile, and be a villian!")
Joss Whedon, the writer and director of this movie, is responsible for several other superb movies and TV shows. He's one of my favorite non-Christian theologians, not the least because of his sober clarity about human evil. His moral instincts transform the Avengers from two-dimensional comic book nonsense into a three-dimensional adventure about heroes we can really root for, not the least because they don't root for themselves.