Sir Malcolm Jones worked counterintelligence for I.O. during the Cold War. During his service, he served as an Assistant Director and was John Lynch's superior, which caused some resentment between the two. He eventually resigned from I.O. during the 1970's following the death of an undercover operative who was looking into a Soviet super-soldier program using stolen alien technology. After her death, he shoved his director's head through a plate glass window. Jones then went to work as a consultant for MI6, where he was later knighted.

Jones later retired to the Yucatan for about a decade until he was contacted by John Lynch via a computer program designed to get in touch with him should Lynch didn't log into it for six months (who he was in a coma at that time). He was sent by Lynch to make contact with Holden Carver and extract him from his undercover assignment. He contacted the CIA and Department PSI about getting help for the extraction, including amnesty for Holden's crimes while working for Tao, though he didn't reveal Holden's name or the criminal organization he had infiltrated.

He was later kidnapped by a group of Tao's enhanced Blackguards while waiting to extract Carver. He was then taken to a secure facility and tortured by CIA double-agent Lee Caruthers, though he refused to talk. Holden Carver later rescued him, but Jones started to convulse due to his heart condition. Holden couldn't get to his pills in time to save his life before the car they were traveling in was hit by a truck. Malcolm Jones died as a result of the injuries and his heart condition.