So, we're pretty sure that Pepper wasn't in Age of Ultron because they couldn't work out a contract with the actress Gwyneth Paltrow.
We get it, you're very busy.
And the movie was already pretty crowded. But what's the in-universe explanation? Well here's my theory: She left him.
We remember how Iron Man 3 ended. Seemed like Tony had promised to give up being Iron Man.
Mmmm whatcha say.
It was such a sweet moment!
Sure, he drives off into the sunset saying he'll always be Iron Man, but it felt like Tony had pretty conclusively ended the almost-dying-constantly part of his life. For the sake of his relationship with the people he cares about. And then he showed up in Age of Ultron with another suit like nothing had happened.
So, what's the in-universe explanation?
If Deadpool were there he'd say that Joss Whedon doesn't understand character development, but since his film rights are still owned by Fox, let's speculate. Could Marvel decide that Tony went back on his gesture and Pepper left him over it? I mean let's be real, he's a terrible boyfriend. Think it's possible?