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Flynn was a senior agent of the Strategic Scientific Reserve.
- "If they wanted me to feel useful, they wouldn't have made me work with you."
- ―Peggy Carter
When Flynn's phone line rang, an assignment would be given to him and Flynn would deploy the recommended number of agents to complete the assignment. The agents, seeing Flynn on the phone, would stand at attention at their respective desks with a briefcase filled with various items, ready to be sent. Though Peggy Carter was among these agents, Flynn never chose her for a mission in the three months that she was stationed under him.
One night, Flynn and the boys were going out for drinks, leaving Peggy to clean up the office when his phone line rang. The caller directed her to the location of ‘Zodiac’ and suggested she draft 3-5 agents.
After Carter recovered ‘Zodiac’, Flynn attempted to belittle and discipline her for insubordination until the phone rang. It was Howard Stark. Stark said the mission was more a notch in Carter’s belt than a feather in her cap and informed Flynn that Carter was to run S.H.I.E.L.D. with Stark.
Flynn was to inform Carter and ‘let her know you’re honoured to bring her the news’. Carter refused his offer to carry her things out of the office. 
- Strategic Scientific Reserve