While on active duty, Mr. Flynn served as the DARPA program manager for the afloat Navy Battle Management Project, which involved the transition of advanced artificial intelligence technology into prototype demonstrations in operational Navy environments. Prior to that, Mr. Flynn was responsible for Electronic Warfare requirements on the CNO staff. He was the senior author of the 1982-1984 Electronic Warfare Appraisals used by the Navy to evaluate its ability to conduct EW/C3CM. He was a principal member of the Navy Outer Air Battle Study; directed the Electronic Warfare Decoy Study, which set inventory standards for all Navy decoys; originated the Navy operational requirement for Counter-targeting systems; co-authored the operational requirement for Tactical Airborne SIGINT; and developed the requirement for the resurgence of lighter than-air vehicles in the U.S. Navy.

Mr. Flynn also served as the Commanding Officer of the Navy’s largest operational aviation squadron, Fleet Air Reconnaissance Squadron TWO, which conducted sensitive SIGINT operations in support of Navy and National requirements. Additionally, he was the Electronic Warfare Officer on the staff of the Commander of the Sixth Fleet where he was responsible for all Navy EW and reconnaissance operations in the Mediterranean theater of operations. Prior to that, he was the Military Aide to the Director of the National Security Agency and served as a senior advisor on ELINT issues. Mr. Flynn was also a senior project engineer with the NSA Special Signal Collection Organization (MUSKETEER).

Prior to attending the U.S. Naval Academy, Mr. Flynn served as a Third Class Electronic Technician on the nuclear fast attack submarine, USS Sargo (SSN-583).