When Gene hands her the radio, Pepper slowly unfolds her arms and holds it as if it's made of glass. She stares at it, eyes wide and mouth partly open.

That's definitely Tony's voice coming out of the radio, and he sounds thrilled to know that she's here (wherever that is) - and a small part of her is thrilled that he's thrilled.

"Y-Yeah, Tony, it's me," she says a little shakily.

What Tony says unsettles her even more. Tony hates Gene, and yet they seem to be on friendly terms. Tony is telling Pepper not to hit Gene? Maybe they really are in a different dimension. Not only that, he's saying Gene isn't lying, which either means Gene has Tony under mind control again, or she actually is on the back of a giant space turtle, on a different planet, in another dimension...and they can't go home.

"I'm not going anywhere," Pepper replies weakly, and slides back down the wall to sit again.