Falling in love with Tony is a gradual process. She can't separate the stages of it in time, not really, not without cutting corners - all of it is approximation, guesswork. And, really, she doesn't realize that she's passed from one part of the process to the next until much later, and it smacks her in the face, and she's shocked by the delayed reaction. It definitely isn't love at first sight.
Tony Stark is infamous, and Pepper's far from stupid. She interviews for the job because of the pay, and the challenge, because there's none greater than managing Tony. He hires her because…well, she doesn't know. Probably because Obediah says he should.
She learns, later that Tony's gone through P.A.s like hot-cakes. He likes them young and tight and wearing low-cut tops, and usually they're not so much qualified for the position as they are for slipping into his sheets. Pepper's the first one who can actually do her fucking job, and the first one he doesn't really blatantly hit on. And, yes, Tony's attractive, and, yes, they're both still in their twenties then, but no, Pepper is not attracted to him when he calls her and says, "Miss Potts, you're hired."
It's been six months, and that's when Pepper kind of realizes that she might have a crush on him. A harmless little crush, one that she only notices when he compliments her and she beams in an instant. She doesn't know how long it's been going on. On certain days it swells up, and other times she hardly notices it - and more often than not, it's because of his behavior on a given day. Pepper likes to think that she's the one in control with the two of them, because she's the only one who can get Tony Stark to actually do what she says, and he doesn't like disappointing her so when he fucks up he tries to make up for it.
Really, though, Tony's got the overall jump on her. He makes her happy, sad, pissed off. He makes her fall for him, decides when he's going to act out and make her rethink getting so close. And thank God he doesn't really get it, that he's got so much power over her, because if Pepper knows anything about Tony it's that he'll use it to his advantage.
A year into working for him the puppy-love is full-on liking him. It's before she's sort of gotten used to the whole unrequited affection thing, and she gets jealous often and it bothers her a lot that he's not interested in her. She lets little things bother her, because she doesn't quite yet understand why he doesn't want her that way. And there's a couple months that go by where Pepper is perpetually in a state of self-loathing, second-guessing, uncertainty. She makes her first (and only) mistake handling his schedule, and it's her fault he doesn't show up to a board meeting. She thinks about quitting, because she doesn't know if she can do her job well when she's so maddeningly frustrated and jealous. She doesn't go through with it. She never will.
She's not sure, exactly, when she actually falls in love with him. If there's a specific moment where the scales tipped, she doesn't realize it when it happens. She's been permanently at his side for four years, watching him like a hawk, doting occasionally and helping and fixing everything. They have a distinct, unique tempo, something natural that she's never had with anybody else.
Being Tony's assistant is beyond just a full-time job, and Pepper's managed to go on six dates in the past nearly-five years - there hasn't been a second date once, because she's never felt any chemistry (nothing like the one she knows with Tony) and she doesn't feel like dating just for the sake of dating. She's used to him getting too drunk and acting stupid, and she knows when it's time to take him home and put him to bed.
It's New Year's day, at five o' clock in the morning, and she's somehow managed to get him into the backseat of the limo even though she's practically dragging him. When she gets in on the other side she's a little out of breath, and Tony's grinning stupidly and slurring his words.
"Pepper," he mumbles, and for a second he dissolves into giggles. "Imma - keneye…on yerlaaap?"
And Pepper's exhausted but she has to chuckle because she has no idea what the hell he's trying to say. He takes her smile as a "yes" and lies down across the backseat, snuggling his head in her lap. The car ride's a little over a half hour, and it takes him no more than two minutes to pass out. Pepper should be angry and irritated, but she's just perfectly content, and when she's sure he's definitely out she lets her fingers play with his hair, tracing confessions of adoration into his scalp, like maybe they'll penetrate into his subconscious.
And she realizes, right then, that she's so completely in love with him, more in love than she thought anybody could be with anybody or anything, and it seems kind of like that "forever" storybook love that isn't actually a real thing.
When they get home, he has to throw up, and she crouches beside him, sprawled across the toilet and babbling incoherently, and it's the least romantic thing she can think of. And still, she's rubbing his back gently when he groans, wiping his chin with a handkerchief when he says he's okay, almost smiling but forcing severity to her face to let him know that this sort of thing shouldn't be okay. All the while, helping him down the hallway (it takes eight minutes to move him a grand total of twenty feet) and knowing that, wow, this is that forever love thing. She's got that forever kind of love and it's for Tony Stark even when he's at his worst, crawling into bed with breath smelling like vomit, and she internally groans and outwardly smiles.
When she thinks about it, it only makes sense.
And for all the headaches, all the borderline nervous-breakdowns, all the whining - "I don't wanna, you can't make me," sometimes she just wants to rip her hair out - she knows that everything good about him outshines it.
Maybe she's fallen for all of the bad things, too.