In April 1983, after having been offered a job at the White House Science Advisor's office, he was approached by the Intelligence Support Activity to replace the previous U.S. Marine representative as ISA deputy operations officer. He turned down the White House offer, going instead to ISA where he conducted numerous missions as an ISA operative, including being with the team that hunted down and targeted those responsible for the bombing of the Marine barracks in Beirut, which killed 241 servicemen. He retired from the Marine Corps after what he perceived as inaction by the Pentagon towards dealing with this incident.
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After he retired from the ISA, he worked as legislative assistant to Senator Warren B. Rudman during the hearings of the Iran Contra scandal, and was a key staff member in drafting the legislation which created the U.S. Special Operations Command in Tampa, Florida. Following his time as a staff assistant to Senator Warren Rudman he again became involved with global terrorism and the Middle East. Cowan was involved in some of the most famous hostage rescues of the Middle East. One of his rescues, the 1990 rescue of American businessmen in Kuwait after Saddam Hussein had invaded that country, was the subject of a documentary where some secrets about his organization were revealed, such as the fact that organization operatives used fake passports issued by a man in Paris to enter countries where people were being held. This operation was conducted in combination with former CIA director Bill Colby. It also included him being part of a three-man team who secretly met with the Iranians at the request of the White House to lay the formal groundwork for the release of the Western hostages being held in Lebanon. Cowan has a graduate degree in computer science and is a member of Mensa. But he is known internationally for his expertise in planning and executing difficult and often dangerous counterterrorism, intelligence, and military special operations. He was also a Fox News Channel contributor from 2001 to 2016, has been a co-host with Ambassador Dick Carlsonon the radio and television showDanger Zone, and he has written articles for The Washington Times, The Washington Post, The Daily Caller, Breitbart, The Hill, and has been featured in several television shows apart from the documentary such as 60 Minutes, Larry King Live and others. He co-wrote Snatching Hillary, A Satirical Novel with Dick Carlson.