He was the son of Siobhan Cleary. He was the eldest of a large family, having six younger brothers and several younger sisters. His father died prior to 1970. His uncle Seamus was a member of the Irish Republican Army in Northern Ireland.
Cleary joined UNIT in the early 1970s, being appointed at one point to guard the Master's TARDIS, which was disguised as a trailer at a carnival. He was present at Stangmoor Prison, where he shot and killed a prisoner. He was also attacked by an Axon at Nuton Power Complex. One of his fellow UNIT soldiers Billy Boyle, who was a good friend of his, was killed during this incident. He later suffered a nervous breakdown as a result of an encounter with the Devil in Devil's End. Captain Mike Yates sent a letter to his mother telling her of his condition.
He was subsequently taken to the Glasshouse, where he received mental conditioning from the Master to go back in time and prevent the assassination of U.S. President John F. Kennedy on 22 November 1963. The Master ordered him to wear a Soviet military uniform in order to fool the United States of America into thinking that the Soviet Union was responsible for the attempt on Kennedy's life, thus leading to a nuclear war in which hundreds of millions would die.
Before Clearly could do this, however, he was conditioned to shoot Dodo Chaplet, a former companion of the First Doctor and the lover of James Stevens, a reporter who had threatened to expose the Glasshouse. He managed to travel back in time and attempted to seize the rifle from Lee Harvey Oswald. However, Stevens followed him and knocked him unconscious. When James brought him back to 1971, Cleary suffered brain damage and was sent to hospital for permanent care.