Peggy Carter continued her work with the Strategic Scientific Reserve in New York City after World War II, where she was set aside to code-breaking and analysis tasks by her chauvinistic boss, Agent John Flynn, underestimating her for field work for being a woman, as she was not given an assignment during her three months under Flynn's orders.
Flynn received word of the location of the Zodiac, a mysterious biological weapon, and sent agents Miller, Johnson and Wilkes to retrieve it. That same night, the agents returned to the office empty-handed, as by the time they arrived, the car transporting the substance was abandoned.
One of the Analysts at the office ordered Carter to make an analysis of a large number of transmissions between S.H.I.E.L.D. and G.U.A.R.D. for the following day, what would force Carter to spend the night working at the office. However, Carter already anticipated such an order, and handed the complete analysis to her co-worker.
Flynn informed Carter that he was going out for drinks with the rest of the agents, but instead of the expected invitation, Carter received an order to stay at the office and review field reports. While alone in the office, Carter received another call informing of the location of Zodiac, requesting three to five agents to retrieve the substance. Carter used the absence of her co-workers as an excuse to take the mission alone, and traveled to the location given, carrying a briefcase full of field gear with her.
Despite her success in retrieving Zodiac, the following morning, Flynn admonished Carter for her actions saying that the only reason that she was an agent was that people felt sorry for her after Captain America died. In the midst of his tirade, the office hotline rang with a phone call by Howard Stark. Stark told Flynn that Carter needed to go to Washington, D.C., as was going to run S.H.I.E.L.D. with Stark. Stark ordered Flynn to give Carter the news, and let her know how honored he was for bringing them.
Flynn uncomfortably gave Carter the news, and offered her to help carry her personal items out of the office. Carter refused the offer, saying that it had been demonstrated that as always, she didn't require his help.