- “I can't sleep. You go to bed — I come down here; I do what I know. I tinker. Threat is imminent and I have to protect the one thing I can't live without: that's you”
Pepper works as Tony's personal assistant. They are friends, but there's chemistry and a mutual pining between the two.
Tony is experiencing a steady rise in blood toxicity levels and, feeling powerless to stop it, he fears he is dying. He doesn't share this with Pepper, but makes her CEO of his company, takes more risks than usually like he has a death wish and keeps her at arm's length. Pepper gets jealous of his new 'assistant', Natalie (Natasha Romanoff undercover) and takes out her frustration on her. It's only during the final battle with Ivan Vanko that Pepper discovers Tony was dying and they reconcil, finally getting together.
Tony and Pepper are happy together and share a domestic moment, with Pepper busy running the company as Tony is sought out by S.H.I.E.L.D. to form The Avengers in the face of Loki's threat.
Tony is shaken by the events in New York — he suffers from panic attacks and is unable to sleep. Pepper has moved in with him, but is unaware of his plight until they have a conversation and he reveals that he fears he is powerless to protect her. She tries to help him through it but things get tense once her ex-boss Aldrich Killian comes their way, threatening their lives. In the end, they make it out alive and well enough with their relationship strengthened.
Tony creates Ultron, Pepper doesn't show up in the movie but is mentioned. In the end of the movie he mentions building them a farm so they can live in peace.
The Civil War is on and again, Pepper is not in the movie but is mentioned. They're taking a break and according to Tony it's "nobody's fault". They never give a reason for the break in the film.
Pepper finally appears again and they're clearly back together. Tony asks Happy Hogan for a ring to which Happy replies, "I've been carrying this since 2008", implying Tony has been meaning to ask her since 2008. Tony basically asks her to marry him before they leave to a press conference room, probably to announce their engagement.