- "When Lincoln Clay went after the mob he inflicted more damage than all the wars and hurricanes combined."
- — Jonathan Maguire
Jonathan Maguire was recruited out of college by the FBI. His first assignment was in Chicago, but he was transferred to New Bordeaux in 1968. He stayed there until 1986, when he was promoted to Assistant Director of the Criminal Enterprise Branch. He stayed with the bureau until his retirement in 1999. He was assigned to investigate the Marcano Crime Family as well as Lincoln Clay after he launches a war against them.
He tried to have Sal Marcano arrested after a witness of the rampage at Sammy's Bar told him that she saw Sal, Giorgi and another associate leaving Sammy's after the massacre. However, Maguire's efforts were halted by Judge Holden, who was in Marcano's payroll.
- Jonathan Maguire is the author of the Lincoln Clay Case Files.
- Maguire witnessed Ritchie Doucet hanging from Baron Saturday's Ferris wheel.
- If the player fails a mission, a cutscene will often play showing a confused Maguire looking at his files and saying "that can't be how it happened", and other lines to that effect.