truth be told I see only 2 movies coming out of using the Skrulls as the main bad guys (but they can have roles in all 3). What I would like to see is the Skrulls brainwash the hulk in the first one thinking that this will let them role in and take over. We know that Iron Man, Thor and Captain America will be part of the show; Speculation and rumor right now is Nathon Fillion will be Pym and Kevin Pennington as either SHIELD agent Rick Jones or Noh-Varr (or both, see movie 3) will be involved as well (no other names have been thrown out there as of yet). Putting Pym and Stark together would run much like the animated Avengers movies, with each trying to one up each other, but you could also use this as an opportunity to cameo so many heroes (IE: as SHIELD tries to pick up the pieces of the Hulk rampage, you can see Wonder Man, Stingray, Justice, Tigra, Warmachine, etc aiding in the clean up project. You could also see the beginnings of either a Pym alone or Pym and Stark collaboration project introducing Vision and Ultron going on in the background). However, it forces the Project Avenger to fully take flight and the avengers stop both the Hulk and the Skrull invasion force. As a sequel safety, you can see a disguised Skrull (This will give credence too to how much bigger the Skrull infiltration of Earth really is and that the "invasion force" was really only an advance party) reprogramming a computer data base muttering something like; "let's see then how they like this".
Movie 2 could then see the continuing clean up efforts from the "Skrull Invasion" (even though as a viewer you know that the real/full invasion has yet to come). Vision and Ultron can be going about general clean up duties, while the Avengers try to work out their personality issues brought to light in movie 1 (try to learn to be friends or at least just to get along). All the while Ultron (we learn the sequel safety from 1 was that Ultron was reprogrammed to be a slave to the Skrulls and Destroy the Avengers) is discreetly pulling strings from behind the scenes threatening to destroy the Avengers from within pitting Avenger against Avenger, and friend vs. friend (ultimately paving the way for the Skrulls to step in and take over of Earth).
Movie 3 could then swing full into an all out Skrull invasion of Earth since all the the more subtle plans have fallen through. The Avengers may be on the ropes and going to fall to the Skrulls when an unlikely ally is revealed, SHIELD Agent Rick Jones is actually Kree Agent Noh-Varr (placed on earth to ascertain a possible Kree takeover). As the Kree and Skrulls hate each other, Varr offers to aid the Avengers providing what info he has on the Skrulls and how to identify them, route them and fight them off (ultimately leading to an animated or even Ultimate Avengers style type of fight it out between the Skrulls and Avengers).
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