The first draft of The Avengers script is complete. The big boys at Marvel have all read it, now that Joss Whedon is attached to direct it the script will go through a few more rewrites before the final film project is complete.
Ever since we found out that Marvel was going to make movies leading up to an Avengers film it's been discussed that the villain in The Avengers would be the Hulk. If they stay with in the continuity of the comic book the story involves Thor's brother Loki unleashing The Hulk to wreak havoc. Marvel describes the storyline like this,
Loki’s schemes eventually came to include Earth itself and these schemes often drew some of Earth’s superhuman heroes to defend Earth and, often, Asgard itself. He first battled Thor on Earth in modern times after escaping from the tree by making Heimdall shed a tear. Loki was then able to manipulate the Hulk into wreaking havoc in an attempt to lure Thor to Asgard, which inadvertently led to the formation of the Avengers. Thor was one of the founding members of this superhuman team, and Loki often found his goals frustrated by them, even when they appeared close to success.
Now there is a new rumor originating from the gang over at Comic Book Movie that claim The Avengers main villain will be the Skrulls, a shape changing alien race in the Marvel Universe. They have two separate sources close to the films production that say the following.
The Skrulls will ‘brainwash’ and use the Hulk in a similar fashion Loki did in the comics. Don’t expect a full on alien invasion, though; that will have to wait for a sequel. The Skrulls’ role will be largely clandestine, similar to the way S.H.I.E.L.D. operates. … Apparently, the Skrulls won’t be the only alien race to be introduced in The Avengers; their enemy, the Kree, will also have a presence as Earthly allies. This isn’t surprising information, considering a young actor by the name of Kevin Pennington has been rumored to portray a character by the name of Noh-Varr; who just so happens to be a Kree. Though I couldn’t get confirmation that Noh-Varr is Pennington’s role, at his point, all signs are pointing to ‘yes.’