He wouldn't usually admit this, certainly not out loud to anyone but deep down, he misses her. He misses his Pepper, his Pep. It seemed like he had lost everyone, since his behaviour had become more and more erratic as he was dying – Happy, 'Natalie' and even Pepper had gone. He knew why SHIELD were doing this; they wanted their super-hero back. But all he wanted was Pepper.
It was always him and her, like the dynamic duo, working together. He'd be an arrogant play-boy whilst she would be the ever-patient, polite woman who would tend on his every need. He had always known that he didn't deserve her by the way he treated her, never fully appreciating what she does for him. It all changes when he's in capacity in Afghanistan. At night, when he's restless and sleep isn't easy, he begins to see her. It puzzles him at first, and he thinks that it must be because she's his personal assistant, that he can basically do nothing without her. But as the weeks wore on, something stirs inside him. Every night when he sees her face, he finds himself thinking that he wants nothing to go home and be with her again. Without her even knowing, she is giving him something to fight to come home for. So he builds the suit, her beautiful face with her flowing red locks forever in his mind, with Yinsen helping. He takes Yinsen's words to heart when he lays there dying, the life seeping out of him.
"Don't waste this chance at life." And he automatically thinks of Pepper, that Yinsen somehow knows.
When he sees her for the first time, her eyes red from what must be tears, he wants nothing more to pour his heart out then and there. But he's Tony Stark – the same playboy billionaire that everyone thinks he still is. So he keeps his mouth shut, his feelings conflicting within him.
He gradually becomes Iron Man – throwing himself into helping others and begins destroying his weapons, the very weapons that were once the pinnacle of his career. Now he is nothing more than disgusted at them. A part of him is doing all this to try to prove to Pepper that he's changed – he doesn't drink as much, he doesn't sleep round anymore and he tries to prove what he is doing is good. He thinks he's on the right track – she states that he's the only one she has as well and she even makes him an ornament out of the first arc reactor. He allows himself to smile, unseen to anyone.
She pretty much knocks him out of the park when he sees her at the fire-fighters benefit, wearing that gorgeous blue dress with no back, showing off every curve. He barely registers what this agent with a ridiculously long name for a division is saying next to him, before he's walking over to him, still stunned. Next thing, they are dancing then they are out on the balcony and he thinks she's about to kiss him before she stops. He's disappointed, because he thought this would be the moment that he'd finally say what he's wanted to say for months. But the moment's lost, and he unintentionally leaves her there. Well, it's not his fault that Obidah has decided to deal underneath the table.
The next few months pass in a blur – Obidah is dead, the whole world knows he's Iron Man and he's now dying. He knows he's running on limited time to tell Pepper how he feels, how many months he's been in love with her.
He tries to put it his meaning when he tells her "it's you. It's always been you." But he knows that she only thinks it's about succeeding him as CEO. He tries to tell her on the plane back from Monaco, cooking an omelette especially before suggesting heading to Venice. He could tell her then; he could even tell her when she asks what he is hiding from her. It's a perfect opportunity – but again, he finds he can't. Maybe he is still the same Tony Stark that he was before he was captured. He loses her, gradually. He's still in his luxury house whilst she's away doing the job he's supposed to do. She doesn't visit anymore either, not wanting to see him. It hurts, more than any other woman has hurt him before. It's then he realises the deep extend of his feelings, and again, he tries to tell her when he visits her at Stark Industries. He stupidly brings along strawberries, the one thing she is allergic to but he didn't know that! She dismisses him, as he's babbling away, trying to make the correct words come out of his mouth.
"I need you…to leave"
"I need you too, that's what I've been trying to s-" his words trail off as he realised what she was actually saying, and at the realisation of what he had just said. They both just sit there, eyes locked together, the tension increasing before they are interrupted and again, the moment is lost.
The next time he sees her, he's at the expo, confronting Justin Hammer, determined to make things right. He knows Vanko is behind all this, and he barely gets another glance at her before all of the drones, including Rhodey are after him. The next time he sees her after that, they argue a little over the fact he never told her he was dying – and he has renewed hope. The worry in her voice, the fact that she actually cared that he never told her makes him believe that maybe, just maybe, there's a chance.
When all of the drones start counting down, he only thinks of Pepper. He knows she's in danger and he suddenly rocketing off, making the suit as fast it can possibly go, whilst all the while, he's thinking "no no no, not her, please not Pepper." He reaches her just in time, securing wrapping his arms around her before taking off just as the nearest drone explodes.
He tries to maintain his focus whilst she's going on about quitting and he finds himself taking her hand in his mechanical one and stroking it slightly.
"You deserve better," He says, feeling a little sense of defeat, "You've taken such good care of me. I've been in a tough spot, and you've got me through it." It's true she has. He may not have seen her, but the very thought of her has kept him going. Her next words pass him in a blur and he's suddenly aware of how very close that are. He takes no chances and whilst moving his hand containing her's closer, he presses his lips to hers, cutting her off.
It's wonderful. It's more wonderful than he could ever have imagined, as he feels the softness of her lips against his. She responses almost straight away, her hand going up to his hair before moving to rest on his chest plate, whilst his hands have moved to rest on her waist and her back. They share a couple more kisses, and he savours every kiss he gets. It puts him in a daze, that he's finally got there, finally showing her what she means to him. They break apart, and a smile graces both their faces. He asks if it's weird, cautiously but she replies breathlessly, he knows that it's okay.
"It's okay right? Run that by me again." He says that just to get another kiss of her and she does not object, meeting his lips once more before they are interrupted (rudely may he add) by Rhodey. When he leaves and they are alone once more, he kisses her again, not wanting to stop. He wants to say it because he's wanted to for so long but he knows, by the look on her face, that she knows. Taking her face in his hands and kissing her once more, she knows that Tony Stark is completely and utterly in love with her.