Jones was born at 8 Quality Row, Shotton Colliery, Easington. After Cambridge, he worked initially in education and joined MI5 in 1955, where he rose to become director of F branch (counter espionage). In 1981 the prime minister Margaret Thatcher, made him director general of MI5. According to Peter Wright, this marked a shift away from the external (Soviet) threat to the 'enemy within'. MI5 now targeted groups thought to be a danger to national security: miners, left-wing trade unionists; CND and the Council for Civil Liberties - what Jones called the 'far and wide left'.
Shortly after Jones became director-general, Mrs Thatcher learned that Anthony Blunt, keeper of the queen's pictures, had confessed to being a Soviet spy fifteen years before. Jones advised that the matter be kept quiet to encourage other spies to confess. Thatcher rejected this advice and unmasked Blunt on the floor of the House of Commons.
Jones also had to deal with the embarrassing Bettaney case which cast some doubt on MI5's vetting procedures and vigilance. Though not personally criticised, Jones resigned in 1985 and subsequently served as chairman of Civil service selection boards.