Can someone explain to me what happened in all of Marvel after Civil War? What happened in Secret Invasion, Dark Reign, H.A.M.M.E.R. and Norman Osborn, how Tony got hurt. And anything else that was big. I've read all of Brubaker's Captain America( I'm currently on 608) and I read Siege. But I feel like I have missed so much. Any help is appreciated.

Oh and can someone tell me which to read first outta Age of Heroes, Avengers, Secret Avengers?

There really isn't an order to Heroic Age, because its not really an "event". Secret Invasion had the rise of the Skrulls looking to conqueor a new world after they lost most of their empire during Annihilation. Osborn rose to power because he killed the Skrull Queen, effectively ending Secret Invasion. HAMMER was basically SHIELD, but more proactive then reactive, it also consisted of foot soldiers from AIM and HYDRA. Dark Reign was pretty much just having known villains taking over the mantle of the Avengers and going after the heroes with government backing, so sorta like Civil War but villains pretending to be heroes while they still hunted the unregistered heroes. Tony got hurt because all through out Dark Reign he was going around the world basically erasing his memory because Osborn wanted to get at the knowledge in his head that would unlock the Iron Man Armor that was in his possession as head of HAMMER. Towards the end of Most Wanted Osborn finally meet up with Tony and beat him half to death, which was broadcast all over the world and started to show the cracks in Osborn's sane facade.
 
That's pretty much a quick summary of everything leading up to the current statis of Marvel, there is a lot missing, but those are the big points I think.