MacMichael resigned from the CIA in July 1983 because he felt the Agency was misrepresenting intelligence for political reasons. His public resignation from the Agency gave credence and notability to his vocal indictment of the Reagan Administration's policy toward Central America. He was considered the "key witness" in Nicaragua v. United States. The case was heard in 1986 before the International Court of Justice, which ruled that the United States had violated international law by supporting the Contras in their war against the Nicaraguan government and by mining Nicaragua's harbors. MacMichael also testified in front of Congress on this matter.
A former investigator for the Christic Institute, he was an outspoken critic of the Institute's reliance on conspiracy theory, arguing that the Institute "was eager, perhaps overeager, to demonstrate that this enterprise [a "secret team" of conservatives] was responsible for everything since Cain slaying Abel. In July 2005, he testified at a special joint hearing of Congressional and Senate Democrats about the consequences of the Plame affair.
MacMichael is a member of Veteran Intelligence Professionals for Sanity (VIPS), founding member of Association of National Security Alumni and the Association for Responsible Dissent, and an outspoken critic of the Iraq War and the Bush Administration. He has participated in six documentary films from 1988-2003. Journalist John Pilger has described him as a "CIA renegade.