Following Marvel's Civil War, the superheroes of Marvel's United States found themselves offered a choice: Either register their secret identities with the government and become federal employees, or else consider themselves criminals and be hunted down like rabid dogs if necessary. Of course, with Iron Man in charge of that latter operation, things never really got that bad - In part because many of the newly-criminalized superheroes were Iron Man's former friends, and in part because Marvel didn't really want to completely demonize the character while he had a movie about to come out. But, following 2008's Secret Invasion storyline, everything changed in the Marvel Universe... and not for the better.
The alien invasion of Earth may have really been stopped by a large number of individuals putting aside their differences and working together, but that didn't matter; former-supervillain-turned-government-department-head Norman Osborn made the very-visible kill-shot by shooting the Skrull Queen dead, and took advantage of the publicity by maneuvering himself into replacing Iron Man as the man in charge of all superhuman activity in America. Which would've been bad enough - Now we don't have someone we can kinda trust in the big seat - but it was made infinitely worse by three facts apparently unknown to anyone else in the US Government:
1. Norman Osborn is insane. As in, takes advice from a mask that he thinks holds the persona of the Green Goblin, even though he was actually the Green Goblin.
2. Norman Osborn leads a secret cabal of supervillains to ensure that order is maintained through various backroom deals, power grabs and in almost all ways, things you probably wouldn't want going on in the real world.
3. Norman Osborn has an agenda.
It's that last one that's particularly troubling. You see, in one sense (and, more importantly, in his own mind), Norman Osborn is a good guy. He wants the world to be peaceful and ordered. It's just that his idea of what that means happens to include some deaths - The Punisher was killed on his say-so - some genocidal activities - He forced the mutant population of America from San Francisco onto a sinking island made of a former asteroid that they're claiming counts as a foreign embassy - and maybe, just maybe, a few disasters that can be made to look like terrorist attacks so that he gets given even more power.
He's not alone in his mission; while his villainous cabal has partially fallen apart (That's what happens when you get a bunch of supervillains into a room together; they backstab and plot), he still has a group of Black Ops supervillains called the Thunderbolts, his own team of supervillains disguised as superheroes called the Dark Avengers, and a mysterious figure whose identity hasn't been revealed but apparently has an impressive superpower or two under their belt. Is that enough to withstand a reunited Avengers team? Probably not, but it's doubtless enough to make the four issue Siege series an entertaining asskicking, amongst other things.