That means some of NA: Illuminati has happened. The skrulls are on their way, baby. Was Hulk spaced pre-NAI?

Also, you could have Steve discovering the Illuminati and going after them. Where has Xavier gone? No one knows. Dun dun dun. He convinced Blackbolt and Namor to stay out of it. He somehow temporarily neutralized Steven (although he's active again in your resistance). Reed just plain got away (smartest man alive, after all). And he captured Tony outright (because he knows ALL the codes).