Even though he won, Iron Man was left massively damaged by the events of Marvel's Civil War. Seen by many heroes - and even more fans - to have trended towards the fascistic in his pursuit of those who opposed the Superhero Registration Act, his placement as Director of SHIELD coincided not only with the return from outer space of the Hulk resulting in widespread destruction across New York City but also an invasion by a race of shape-changing aliens that, again, left large parts of New York City destroyed but more importantly made it clear to everyone in the world how ill-prepared Tony Stark was to be in charge of national security issues.
Forced out of office by the dissolution of SHIELD - Replaced by HAMMER, a similarly acronymized US Government agency - Stark refused to give up the identities of all superheroes under the Superhero Registration Act to his successor, Norman Osborn, leading to Osborn (falsely) accusing him complicit with the alien invasion and an enemy of the state. As Stark went on the run, it was discovered that the central database of superhero identities was, in fact, his own brain, altered by the Iron Man armor. Convinced that Osborn would stop at nothing in order to get this information, Stark orchestrated a slow wipe of his entire brain that left him in a vegetative state under the medical care of Donald Blake, the human alter ego of Iron Man's fellow Avenger, Thor.
With the assistance of Thor, the Black Widow, long-time Iron Man companions Pepper Potts (Now in possession of her own Iron Man armor) and James Rhodes (AKA War Machine) and a returned Captain America, Tony Stark was "rebooted" from a backed-up version of his own brain, and reborn as Iron Man just in time for Siege.