Since arriving, Pepper had been with the other Tony as he attempted to work out a solution to the Extremis problem. She wanted the Extremis removed if it was at all possible. She didn't feel herself and she wasn't comfortable in her own skin. She was afraid of contact because she was afraid of burning the person that touched her. She just wanted to be herself again.
Pepper reached the Tower and found that she had access and she headed up to the conference room, knocking on the door as she opened it and peeked inside. "Tony?"