In a nutshell after Osborn took over SHIELD and renamed it HAMMER, Stark was discredited and blamed for the Secret invasion of the Skrulls based on his "inability to prevent a secret infiltration and invasion" of Earth and because the Skrulls disabled all StarkTech equipment and technology. The Avengers were disbanded and Osborn took over the Initiative.

Afterward Stark uploaded a virus to his former computer systems to destroy all records from the Registration Act, so that Osborn couldn't know the identities of the other heroes. The only known copy of which is located in his brain. He's currently on the run from Osborn's forces in one of his extra armors and deleting this information piece by piece, but is also causing his mind to deteriorate. Osborn currently controls the other Armors in Stark Tower. With his mind going to pieces he's finding it harder and harder to control all the equipment in his armor and has been downgrading his armors to easier control them.
Source(s):
http://en.wikipedia.org/wiki/Tony_Stark#Secret_Invasion
http://en.wikipedia.org/wiki/Tony_Stark#Dark_Reign
Comic geek. ^_^


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