Originally Posted by LokiDionysos
I think he thinks she's dead like Happy and thinks she died at the same time, but the bad guys move her. Part of why he's so depressed. Happy is actually dead and then he'd find out Pepper survived, was made a subject, had the arc reactor put in her chest a little later.
Hmmmm thanks for that clarification, I guess it's all in the execution now (If true)