After accepting a commission in the United States Navy in 1944, McGonagle held various assignments before taking command of the "Liberty" in 1966. In June 1967 the "Liberty" was sailing in international waters in the Eastern Mediterranean when it was attacked by the Israel Defense Forces, injuring McGonagle, killing and injuring other members of his crew, and severely damaging the ship. He maintained control of the ship until help arrived, and after healing from his wounds was awarded the Medal of Honor for his actions on the "Liberty" in 1967. He continued his navy career, holding several more positions until retiring in 1974. When he died in 1999 he was buried at Arlington National Cemetery with full military honors a short distance from the graves of some of his crew who were killed during the attack.