A/N This is my version of what might have happened in Iron Man Three after Pepper left Tony. I found it in my fanfic notebook and decided to post it. It was not intended to be posted, so don't hate me if it sucks. Please Review!
What Happened After Pepper Went to Sleep Downstairs
"I'm going to sleep downstairs. Tinker with that." Once Pepper got over her fear, she wasn't really angry, just resigned. It seemed she wouldn't ever be better than Tony's experiments.
Tony shook his head to clear it and stood quickly to chase after her. He didn't make it very far before he stubbed his tow on the torso part of his suit. Cursing, he shoved the pieces under the bed. If he managed to convince Pepper to come back up to bed, she wouldn't want to see the suit still on the floor.
Pepper watched from her spot stretched out on the couch as Tony ran down the stairs, right past her, and halfway out the door before he realized where she was.
He walked back over to her slowly. "Why are you on the couch?" he asked, confused. The Stark home had multiple quest bedrooms. He'd figured she'd camp out in one of those. He told her as much adding, "You of all people should know that."
She propped her head up on her hand and fixed him with a look he couldn't quite pinpoint. "Me of all people? Yeah, I know how many there are. I even know which one's you've spent the night in and with which girl. What I don't know is what you've done in them. Do you really think I trust those rooms?" she raised an eyebrow.
"I haven't done anything in them since. . ." he squinted, trying to find a date, "Well, it was before you," he finally said.
"I know," Pepper said quietly, not looking at him.
"Look, if you are still mad at me and don't want to see me, fine, just please take the bed, and I'll take the couch."
"Tony Stark is offering to give up his custom made, therapeutic bed in favor of a couch that is definitely not made for comfort."
"Captain America isn't the only one capable of being a gentleman," he huffed.
"No, you're right. Hawkeye is pretty sweet, too."
"Pepper. Please just take the bed."
"Will your suit attack me again?"
"No, it wasn't supposed to do that. I'll check the sensitivity and add a default so that it won't respond when I'm sleeping. But what if I'm unconscious in a hostile environment? It also obviously thought you were causing my distress . . . I'll add a setting so that it won't attack you no matter what. That will take ID technology and more advanced sensory details. I'll need – "
Pepper interrupted before he got going. They both knew he was talking more to himself than to her anyway. "That's the thing, Tony. You build suits, you build robots, and you talk to JARVIS. They're great, but they're no human. I'm worried about you, and you won't talk about it. You don't have to tell me everything, but please at least stop acting like everything is okay," she rose and crossed to the stairs, before turning to look at him. Tony was still facing the couch where she'd left him. "You need some time to figure things out. I'm not really mad, I'm not giving you any kind of ultimatum, but you need to figure out what is most important to you and let me know," she left him with a lot to think about.
~o0o~
Of course Tony knows what his priorities are. But what was bothering him was that he had managed to convince Pepper that his suits were more important to him than her. And she was right, he could open up more. He'd just gone so long without anybody that he'd forgotten that someone might actually care.
Pepper was lying on her stomach when Tony came into the bedroom a few hours after Pepper left him to think. He stopped a minute at the edge of the bed, just to look at her. She looked so beautiful. He slid back the covers and snuggled up close to her, wrapping an arm around her waist and kissing her neck.
"That had better be Tony," Pepper said, her voice muffled by the pillow her face was pressed into.
"You," he said into her neck.
"What?" she finally turned around to face him.
"You are the most important thing in my life. Don't forget it and –dear God– don't let me forget it!"
Pepper smiled, "I won't," and kissed him. Tony pulled her close and fell asleep to the sound of her breathing and the feel of her heart beating against him.