Inspired by stories about her Aunt Peggy's adventures in the French Resistance alongside Captain America, Sharon Carter joined the newly-formed espionage agency S.H.I.E.L.D. During an early mission against Hydra, Sharon was attacked by the mercenary Batroc and aided by Captain America. Initially knowing her only as Agent 13, Cap worked alongside Carter on several subsequent missions against A.I.M., the Nazi Red Skull, and others; the two soon became lovers, and Cap was also reunited with Peggy Carter, helping her recover from mental despair. Eventually, Sharon was assigned as liaison to the NYC police while investigating the terrorist organization called the National Force. Supposedly affected by mind-influencing gas, Sharon infiltrated the National Force, and when confronted by the National Guard, was apparently incinerated by the self-destruct device in her uniform, leaving Cap to grieve for her death.
However, Sharon's death was a ruse by S.H.I.E.L.D., which sent her on a top-secret mission; at its end, S.H.I.E.L.D. and its director, Nick Fury, erroneously believed her dead. Abandoned in enemy territory, Sharon spent months imprisoned in the dictatorship of Tap-Kwai. Finally escaping, she spent the next few years as a mercenary, often forced into violent or degrading activity; Sharon's experiences cost her much of her idealism, making her hard and bitter. Infiltrating an organization known as the Kubekult, she learned that it planned to resurrect Adolf Hitler via the Cosmic Cube, and Sharon became the unlikely ally of the Red Skull, who opposed the cult for his own reasons. To aid them, the Skull revived the temporarily comatose Captain America, who was stunned to learn of Sharon's survival. Although Sharon, still scarred by her experiences, attempted to keep her former lover at a distance, she continued to work alongside Cap against such opponents as Nightmare and Count Nefaria. She also rescued Nick Fury, believed dead, from a pocket dimension he had been trapped in during a mission.
Initially maintaining her freelance status, Sharon next served as S.H.I.E.L.D. Director while Fury was on assignment. Following his return, she resumed her position as S.H.I.E.L.D. agent, and she and Captain America fully reconciled and considered renewing their romance. However, their relationship again became strained when Cap learned of her reluctant involvement with S.H.I.E.L.D.'s anti-mutant Contingency, and the couple again parted ways.
In the aftermath of enactment of the Superhuman Registration Act and the subsequent super-hero Civil War, Captain America surrendered, and was brought to the Federal Courthouse in New York City to face his arraignment. Sharon escorted the Captain, unaware that she had been brainwashed by Dr. Faustus who had infiltrated S.H.I.E.L.D. posing as Carter's psychologist. In a plot engineered by the Red Skull (secretly alive within the mind of ex-Soviet general (Aleksander Lukin) with Faustus and mad scientist Arnim Zola Captain America was shot first by a sniper, Crossbones, then subsequently by Sharon several times at point blank amid the chaos. Oblivious to firing the gun, Sharon accompanied Captain America to Mercy Hospital where he was pronouned dead on arrival. At the hospital, the Red Skull's daughter, Sinthia, spoke the keyword to release Faustus' hold making Sharon aware, to her horror, of what she had been programmed to do.