Virginia "Pepper" Potts was Head Administrative Aid to Tony Stark and a loyal assistant. She was often like a nanny telling Tony what to do, but always with some small amount of admiration that later bloomed into a more romantic interest.

Pepper was sent to hack into the company computer system when Stark became suspicious of his former mentor, Obadiah Stane. Once in, she discovered that Stane had been supplying terrorists with Stark weaponry and had hired the Ten Rings to kill Stark. She later met with Agent Coulson of "Strategic Homeland Intervention, Enforcement and Logistics Division", a counter-terrorism agency, to inform him of Stane’s activities.

When Stane attacked Tony on the roof of Stark Industries, Stark instructed Pepper to blow up the reactor core. Initially reluctant because she didn't want to hurt Tony, she soon complied, causing a blast that destroyed Stane’s battlesuit, and killing Stane himself. Stark also survived the blast, after being caught in its periphery, although it took some effort on Pepper's part to rouse him from his stunned state.

Six months later, Potts was promoted to Stark Industries' CEO while Tony was getting his affairs in order. Unbeknownst to her, he had developed terminal complications from the poisonous side-effects of the arc reactor's palladium core. As a result, he began to spiral out of control and eventually his increasingly reckless behaviour pulled them apart entirely.

Their reconciliation came on a night when Stark's arch-rival, Justin Hammer, unveiled his latest military marvel, a series of humanoid combat drones. When the drones activated and attacked Stark, apparently of their own accord, Pepper and Natasha Romanoff confronted Hammer and demanded they be shut down. When they found that Hammer had lost control of them, Romanoff departed to deal with them while Potts remained at the expo. Stark swooped in and saved her when she strayed close to one of the damaged drones right before it was about to explode.

With Stark back, and free of the toxins in his bloodstream thanks to a new arc reactor design, Potts quit as CEO of Stark Industries. When talking to Nick Fury, Tony also hinted that he and Pepper were in a relationship and his life was back on track. This eventually graduated to a live-in arrangement when she began sharing living space with him in Stark Tower.