There is a lot in his life that Tony Stark doesn't remember. He has the usual infantile amnesia-no memory of his early childhood. He is rather prone to concussions, a regrettable side effect of the career he has chosen and the moments leading up to them are often, though not always, forgotten. He is the sort of high profile personage that people want to target in general, so he's also got quite the list of non-superhero inspired personal attacks that have resulted in a head injury or a chunk of missing memory here or there. (The superhero part always comes in very handy in resolving these matters.) The situation he has found himself in now is different-years of his life are gone and it's his own damn fault.
It's his own damn fault for a lot of reasons.
The concept of making a back up of a human brain was something that fascinated Tony for years, but he was always just ethical enough to refrain from actual experimentation. The Iron Man had a long list of enemies who were not so ethical-Advanced Idea Mechanics, Roxxon Energy and the like, and he...well, when the opportunity arose, he was willing to liberate their research. And when he had a spare moment here and there, he was willing to perhaps give reverse engineering it a go.
Tony Stark is capable of creating a mechanical backup of a human brain and booting it up as a fully autonomous, non-biological robotic person. He has been capable of that for years. The game changed when Maya Hansen came along with her Extremis enhancile. The last thing he remembers before waking up on the cement floor of an abandoned middle school in hicktown is being of three minds: Part of him had known that he needed Maya's enhancement to survive his latest batch of injuries. Part of him knew he needed it to save the country, because there was a powerful guy with a grudge headed to Washington. And part of him was excited when Maya left the room and it was just him and the nanobots that were going to rewrite his brain. Because now he had the chance to rewrite them.
He told her that she is smarter than he is.
If she was anywhere near as smart as he was, she never would have left her technology alone with someone like him.
So, he created the brand new Tony Stark, but before he did that, he made a back up of the old Tony Stark because you never upgrade without backing up your data first. That's just good sense.
Something else that is good sense is periodically saving your work, so that if you have to restore from an older version, you have the most up-to-date older version possible. Apparently (unsurprisingly) the new Tony Stark was an arrogant SOB who never thought he'd need to restore from an older version. Never saved his data again.
And even that could have worked out fine-human beings have existed for untold generations without ever needing to restore their data-but he screwed up so badly that he had to erase all of his sensitive information.
Information that should have been safe and sound, locked up in his brain. But the mind is not without its weaknesses and the whole thing had to be wiped clean.
Restored from an old back up, there is a large chunk of his life that Tony Stark doesn't remember. He looks in the mirror and he person he sees is too old to be himself. He reads about himself in the newspaper and on the political blogs and he doesn't recognize himself. He wears the armor and they call him "Stark" because the whole world knows who is underneath the faceplate. He looks his brothers-in-arms in the eye and he doesn't see love.
There is a lot he doesn't remember. And he is used to being told about his actions, used to forging some kind of second-hand emotional connection to events that may or may not have occurred they way he hears about them. Used to being ashamed of the ruins more than ashamed of the actions themselves. All of that is just another day in the life of Tony Stark: Alcoholic.
He usually doesn't give the drinking blackouts the weight they deserve. When he was young, he accepted them as part of the fun, wished he could remember the craziness and moved on with life and mid-afternoon martinis. Later on, he moved into the denial stage-it wasn't he who had the problem, it was everyone else. He pretended the blackouts didn't happen almost long enough to believe it. When he (finally) got sober (for this latest time), they became one of those things he just doesn't talk about. He finds it worked better for him to steer clear of the temptation and anything relating to it than retell the same old stories about why he should abstain. After a while, and in the biased perspective of someone who sort of wants to fail, the horror stories start to sound fun.
There is a lot in his life he doesn't remember; some for good, some for ill, some for arrogance, some for alcohol. He doesn't remember joining the new Avengers along side Spider-Man, a young man who was like a son to him once they got to know each other. And he doesn't remember the utter destruction of that relationship. He doesn't remember thinking it would be a good idea to clone Thor and he doesn't remember that clone's murderous rampages. The latter he hears about in the news, the former is one of those tiny human things that no one else ever finds significant enough to mention. He doesn't remember the time Ultron hacked into his biology and turned him into a woman, nor does he remember that the Avengers promised to make fun of him about it forever. All these events, Tony doesn't remember because he was too arrogant to save them.
Once upon a time at a party he can't recall, he coaxed his secretary into dancing with him. It started out stupid and fun and harmless, but things between himself and Pepper have a way of not staying so simple. Tony doesn't remember grabbing Pepper by her hips and pulling her flush against his body, or telling her in front of a room of strangers that he'd eat her pussy all night long if she asked him nicely. Or, hell, she didn't even have to ask, he was about ready to do it anyway. He doesn't remember her mortified and a bit afraid, scrambling madly for the nearest thing to grab onto. All she got her hands on was a flute of champagne from a passing waiter's tray, which she threw in his face. He doesn't remember what he said to her after that or ever once consciously thinking that he had some sort of divine right to sex. These events, Tony doesn't remember because he was piss out of his mind drunk.
What he does remember is begging her to come to work, to speak to him, to look at him. He remembers the three substantial and outrageous raises he offered before she accepted and he remembers the excruciatingly long and involved sexual harassment suit that Human Resources strong armed her into filing. If it had been just about Pepper, he'd have given her anything she wanted, but he let his lawyers fight back because she didn't want any of it to happen. She just wanted to forget about the whole event. Unfortunately, there had been a roomful of witnesses and she knew that she had the responsibility to do the right thing. Pepper Potts was a powerful, high-profile woman working for an even more powerful, high-profile man. She could not allow his behavior to go uncontested, not with a world of less powerful women watching and taking their cues from her. Looking back, it was probably the agonizing mutual discomfort of having their entire relationship under a microscope that repaired their friendship more than anything. The settlement was 2.5 million dollars to Pepper-her lawyers expected to get a lot more money out of Wealthy and Promiscuous Playboy Anthony Stark, but she had kissed him-really kissed him-once in front of reporters and the photographs hurt the case. The amount was inconsequential to Tony and Pepper never once mentioned what she did with the money.
By the time six months had passed, only two things had really changed. Pepper never, ever went to company-sponsored social events anymore and she never, ever tolerated him when he was drinking.
Tony learned about a decade later that she and her then-ex, now late, husband had financial problems after leaving his employ. Pepper never struck him as the kind to squander money, so she likely didn't keep the settlement. He has never wanted to drudge up old demons and ask her what she did with the money. Probably, she donated the whole lot to a charity and got on with pretending the whole affair never happened. Also-within a few months of Tony learning of that gem, she offered to accompany him to a party he was hosting in Seattle. So, ten years and sobriety later, things were really and truly back to normal. She managed to pretend so well that they came dangerously close to crossing the point of no return several times in the months to come, even though she was probably the last woman in the world who should ever consider it. They had learned one thing from the whole ordeal, though. Everything that happened, almost happened or didn't happen between them happened in private and they never discussed it afterwards.
All of this, he remembers with great clarity and a whole gamut of first-hand emotion. The very last thing he remembers of Pepper before waking up in that basement is that she was willing to touch him and she could do so freely, without self-consciousness, shame or fear. Their intimacy was an irrevocable part of who they were and he accepted as fact that it would always be so. And while that final, physical congress remained his private dream, Tony was not unsatisfied with their emotional closeness or with what simple touches they shared.
But there is a lot in his life that he does not remember and Pepper Potts is very, very practiced at keeping these things to herself and very, very good at pretending certain events never happened. They are both very capable of keeping the things that they do not want exposed to the rest of the world behind closed doors. If there are no witnesses, there is no one to tattle, even to a participant.
Once upon a time, after a fight he can't recall, his former secretary complained that she was absolutely rancid as her Starktech armor split itself open and let her out. They kissed-innocently kissed-before he pointed her to the shower and promised to find her a towel and clean clothes. The towel was easy, but the clothes were his. Tony didn't have any women's undergarments on hand, a fact which he wasn't sure would be welcome or met with dismay. It was hard to predict which she would find worse-panties of unknown origin or being expected to go without in borrowed clothes. He left the towel, tank top and drawstring sweats on the floor near the shower stall. While he did it, Tony looked wistfully at the curtain. He couldn't see a thing, but he knew beyond a thin film of plastic, she was naked and wet and visions crept into his mind anyway.
Sometime later, when Pepper emerged from the bathroom, she was wrapped in the towel, her hair dark and heavy with water. He watched from the couch as it dripped from the tips of her hair, to her bare shoulders and ran in thin streams down to the towel. He had been working on something-he had absolutely no idea what anymore, but there was a clipboard already in his hands and it was terribly useful for hiding his crotch. Very softly, Pepper told him that she was tired. He was unable to conjure a response to that, so silence hung between them until she bit her lip and asked where his bed was. He pointed, vaguely, because he was transfixed, lusting for her fiercely, and the damn thing was plainly in the same room as them. As she padded towards it, Pepper asked if he intended to join her. He had no answer to this question-his muddled, partially-erased and infinitely distracted mind barely even comprehended it-until she dropped the towel.
From there, it took very little direction before his head was between her legs and his name was on her lips.
Disclaimers: Owned by Marvel. Based mostly on Matt Fraction's work with the characters, but there is some stuff from earlier runs, too. Woot.