After Tony Stark had a one night stand with Christine Everhart, Pepper greeted her the next morning with her clothes and escorts her out. A few hours later, Tony went missing. Pepper is shocked to hear the news and she and Happy tries everything they could to find Tony.
After Tony escaped the terrorists, he is picked up by the US Armed Forces led by Rhodes, Pepper and Happy happily welcomes their boss back with Pepper crying before him, saying that she's glad Stark's back because it was very hard for her to find a new job.
Pepper accompanies Tony to a Burger King and orders for a press conference. In the press-con, Stark announces that his company will no longer manufacture weapons, along with Stark they then storm their way out of the place.