In the Comics

Tony Stark and Pepper Potts have been a number of things to each other through the years. Early in Iron Man’s career, Pepper served as Stark’s secretary and harbored a deep desire to one day become Mrs. Anthony Stark. Since then, both Tony and Pepper have experienced countless changes, and though they sometimes drift apart they inevitably return to orbit each other’s lives.

When we first met Pepper, she had already become Tony Stark’s personal secretary after proving her value by pointing out an accounting error made by Stark himself. At first oblivious to her flirtations and thinking of her only as a secretary, Tony eventually realized how deep Pepper’s emotions ran but had to keep her at a distance because of his secret life as Iron Man.

During a fight between Iron Man and Titanium Man, Pepper realized her love for Happy Hogan when he almost died trying to save Stark’s life. The two dated for a short while before eloping, effectively putting an end to any possibility of a romance between Tony and Pepper…for the moment, at least.

Pepper eventually left Tony’s employ, but came back to work for him once more, putting a strain on her marriage with Happy with her long absences from home due to Stark’s globe-trotting business affairs. During a fight, Happy revealed Tony’s secret identity to Pepper, creating a rift between the two. Pepper eventually moved to Colorado with Happy, and out of Stark’s life.
During Tony’s personal war with Obadiah Stane, who had taken control of Stark’s company, Stane kidnapped Pepper in order to strike at Iron Man. Though he eventually rescued her, Pepper asked Tony to stay out of her and Happy’s life, as they couldn’t risk being involved with someone so dangerous now that they had adopted two children.

For a long while Tony and Pepper’s paths completely separated. But upon his return from the Heroes Reborn universe, Stark set out to re-establish his company, and he called upon his two closest and most entrusted former employees to help him do it: Happy and Pepper. Since leaving Tony’s life, however, the couple had divorced and lost custody of their children.
Tony’s friendship with Pepper became stronger than ever during this time, but it remained strictly that: a friendship. Her relationship with Happy eventually blossomed once more and the two remarried.

During the super hero Civil War, the Spymaster attacked Happy in and left him brain dead. Pepper asked Tony to help end her husband’s life by using his control over technology to shut off Happy’s breathing apparatus in the hospital, but he refused. Shortly after, Happy died, though whether Tony had anything to do with the event remains unclear.

Pepper went on to work under Tony once more as part of the Fifty States Initiative. Taking the codename Hera, Pepper led California’s super hero team the Order. Pepper was fatally wounded after Ezekial Stane attacked a building where Tony was attending a party, forcing Tony to save her life by placing a mag-field generator in her chest  similar to the device that kept him alive during his early days as Iron Man.

The generator also gave Pepper extra abilities such as levitation, and when Stark named her CEO of his company while he went on the run from Norman Osborn she also discovered that he had developed a suit of armor just for her. Taking the name Rescue, Pepper used the suit to help Tony. During this time, their romance once again flared up, and though they continue to have feelings for one another their relationship remains complicated.

When Peter Parker and Tony Stark traveled to the future in Invincible Iron Man #500, a gravestone with the name Virginia Potts-Stark is visible, suggesting that Tony and Pepper finally give in to their attraction and that Tony’s future son Howard is also Pepper’s child.