"Oh... Well I guess that makes sense." Actually it didn't. Not at all really. But Pepper didn't want to let on that she thought so. She also hid the fact that Tony finding getting muddy 'fun'. What had happened to him.
"I have to ask, you didn't hit your head when you got here, did you?" It was better than asking if he was a pod person. Or Who are you and what did you do with the Real Tony Stark.