Secretary to Tony Stark, Pepper Potts is disappointed when her boss introduces her to his new chauffeur Happy Hogan, whom she finds repulsive despite the man's attempts to charm her. She openly tells him that she is waiting for the day when she will become Mrs. Stark. A week after Stark has fired Professor Shapanka, the plant is visited by Jack Frost. Pepper warns her boss that the villain is after him but he freezes her right away. She and Happy are unfrozen after Iron Man has forced Jack Frost to surrender.
With the menace of Mr. Doll forcing wealthy men to sign their fortunes over to the villain, the authorities have Tony Stark under surveillance so the playboy uses Pepper's infatuation over him to escape the guards, much to her disappointment.
To impress her boss at an employee dinner, Pepper has gotten a whole makeover and from now on, she no longer leaves her freckles uncovered. When Tony Stark is forced to cancel his presence at that dinner, she asks Happy to be her escort. Yet at the ball, Pepper gets annoyed that Happy would make even make it look like they are together.
During Iron Man's absence, Happy is injured by the Unicorn who has broken into Stark Industries and ends up in a hospital. The villain captures Pepper to lure Iron Man who comes to her rescue. Next day, she is truly relieved to hear that Happy is out of danger and she tells him that she misses him.
Tony Stark finally asks her out but he only takes her for a walk in Coney Island. Disappointed, she accepts a date with Happy the following day to let her boss know he's not the only man around and that she was far from impressed by her date with him.
Tony Stark has locked himself up in his office after a sudden illness, which makes Pepper terribly worried. When finally Iron Man tells them that their boss has left town and put him in charge, Happy and Pepper get suspicious.
Tony Stark informs Happy and Pepper that the recent sabotages in his factories are liable to lead his company to bankruptcy but they both choose to say with him.
Happy and Pepper are worried that Iron Man may not be able to save Tony Stark from the Melter.
Pepper deliberately causes Tony to miss a date with a woman. She realizes he boss got wise of her maneuver when he gives his tickets to a show to Happy and her.
Pepper's is rightfully suspicious when Madame Natasha shows up at the plant to meet Stark again and steels a prototype invention.
When Stark is summoned to the Pentagon, Pepper fails to convince him to take her along.
While Stark is away, Pepper is making sure that Happy busy managing the plant.
After Pepper makes fun of Happy's jacket, they both get the visit of an injured Captain America who came to see Iron Man. When Cap disappears, they use Stark's tracer to locate Iron Man and tell him about it. They find him at a power plant where they both dangerously get caught a battle between the two Avengers.
As officials are getting concerned about Tony Stark's whereabouts, Happy and Pepper are worried that something terrible has happened to their boss and suspecting that Iron Man is hiding something. Hawkeye breaks into Stark's factory and takes Pepper hostage until Iron Man chases him away. Then she stops Stark's security guards from shooting Iron Man because she is still not convinced of his guilt.
After one month of Stark's absence, they both give their resignation to Iron Man and help the police investigate on the Golden Avenger. Happy finds their ex-boss alive in his bed at home. When Pepper arrives, Stark tells them that the doctor ordered absolute rest, yet he and Pepper still don't trust Iron Man. Right after they leave, Stark's house is destroyed by a strange ray and everyone is convinced that he is dead.
After a few weeks, Stark shows up at the plant, putting an end to the allegations of his death. He announces to Pepper and Happy that he secretly got engaged to a Boston debutante, much to his secretary's disappointment.
During a date, Happy proposes to Pepper, but even though Stark is now engaged, she needs more time to forget about him. On their way back, they are captured by the Black Widow and Hawkeye. After Iron Man has rescued them and their boss shows up unharmed, Pepper is relieved to see him.
She sees what happens to Iron Man in the news and believes him dead.
When Happy decides to quit his job, Pepper realizes that she misses him and blames Iron Man for hogging all the glory. She phones Happy at his grand-father's home in Ireland and convinces him to come back.
Happy invites Pepper out to dance, but although she accepts, she also offers their boss to come along. Some time later, Pepper hands to Tony a telegram from beyond the Iron Curtain in which the Titanium Man challenges Iron Man to a broadcasted fight. Some time later, Iron Man has accepted the challenge and Tony invites Happy and Pepper to Alberia to attend the event. At the hotel, she gets jealous when she spots Countess Stephanie de la Spiroza, one of Tony's old flames. As the battle begins, Pepper realizes that the Communists have cheated and set up a mine field. At the second round, she watches as Happy rushes to the battleground to hand something over to Iron Man but gets critically wounded by Titanium Man. In total shock, she faints. As she comes to, she cries as she sees the ambulance leave with her comatose friend. At the hospital, Pepper gets a grim prognostic from the doctor and holds the Countess responsible for stealing the device that got her friend injured. Questioned by Pepper about his absence during the fight, Tony comes up with a lousy excuse and realizes that she now despises him.
