Within seconds of Tony announcing that Pepper is the new CEO of Stark Industries, the stock tanks. It actually manages to dip further than when he made it clear he was serious about not producing weapons any longer.
Pepper would like to say it doesn't shake her confidence. She only lies when it comes to business.
After some deliberation, she fires three-quarters of the executives directly below her. They get hit with a discrimination suit—which legal files a 12(b)(6) on and has dismissed before it can begin—and she thinks Tony's got to notice this, figures she's about to get fired as well.
Which, fine, if she can't do the job her way, the way it needs to get done, she's willing to accept not doing it at all. Not that she has any idea what she will do, but there's never been a time she hasn't landed on her feet. That is not a concern.
Tony does notice, although a week later than she would have expected. He says, "I never really liked those guys anyway," and that is his whole opinion on the subject.
She asks, "Had you actually met any of them?"
He looks up from whatever he's tinkering with and says, "Not the point."
She sighs. "What is the point, then?"
"They weren't listening to you. I don't like stupid people working for my company."
Pepper closes her eyes, forces down a smile. Tony's been pissing her off for weeks now, this isn't going to win her over. She does ask, "Will that be all, Mister Stark?"
He's slower to answer than usual.
The thought comes to her, later, though, when they've gotten Tony cleaned and bandaged up and he's sleeping on his couch, his head pillowed in her lap. She hates herself for it a bit, but she can't ignore the thought, not really.
She has two options, she decides. She can wait until morning, and tell Tony that this was all a mistake, a moment of panic and relief. She can watch him pass it off as the same, his eyes dark and blank to hide anything else he might be feeling. She can keep whatever reputation she has pristine, have the rumors be based on nothing.
Or she can take what she wants, take Tony, in all his shiny, brilliant impossibleness, and stay his CEO and not give a fuck what other people think or say. Stark Industry's tech sales are up 3% last quarter, despite the market predictions. Tony trusted her with his company—willed it to her, now, she realizes—and she's done well by it. She knows that.
Tired, but alert and certain, she decides that is all that matters.