Proof Positive
Tony is no stranger to paternity claims from his female conquests, there's a system in place for them. But when one of the tests actually comes back positive, he makes a rash decision to not tell anyone about it, not even Pepper Potts. All Mary Parker wants is for Tony to spend a little time with their son, and she'll badger Tony Stark into showing up at least twice a month in any way that she can.
And then he goes missing for three months in Afghanistan. Tony has a lot to think about in his life now, how he wants to run his company, how his life is going to change with the arc reactor, and what he's going to do about his son, Peter. Then, the Avengers Initiative pops up, and in waltzes his childhood hero, and enemy, Captain America.
Follows IM1, IM2, Avengers. Not canon-compliant, but follows the plots. Tags to be added as written. Bad summary.