Pepper knew that Tony had been a little off ever since they'd come back from the dead. Though she wasn't quite sure why, she had a pretty good guess as to what the problem was. It was probably a bunch of things, and somewhat her own fault. She'd kind of freaked out about dying and all that. She hadn't meant to hurt him.
When she'd come upstairs and Jarvis told her that he was gone, she wondered where he had gone. After doing some errands and fixing up the house and he still wasn't home, she figured she'd give him a call. So she rang his phone, waiting for him to answer.