- "Sal is a cancer. A leech. The only way to make that right is by killing every cocksucker who's ever looked at that piece of shit."
- — John Donovan
John Donovan graduated from Princeton University in 1953 and was recruited into the Central Intelligence Agency soon after as a paramilitary operations officer. As an operative he was sent into Vietnam where he ran covert operations against the North Vietnamese regular and Viet Cong forces. During an operation in April of 1966, Donovan met Corporal Lincoln Clay, who distinguished himself by controlling the battlefield despite overwhelming odds. Clay ignored his own injuries while retrieving two fallen soldiers, PFCs P. Ellis and Q. Doroquez. Donovan continued to work with Lincoln and the two became close friends and colleagues during their time in Vietnam.
Donovan reunites with Lincoln in New Bordeaux, where he reprises his role as handler and trusted source for Lincoln, supplying him with intelligence and advanced government technology in his effort to take out the Marcano Crime Family. Donovan later left the CIA in 1969 as a result of his actions.
During Lincoln's recuperation, Donovan rented a room at the Blue Gulf Motel which he furnished with surveillance equipment stolen from the FBI, and started running surveillance operations on the Marcano Crime Family and potential assets that Lincoln could recruit to his cause, including a network of civilian informants that he had cultivated to report on the activities and whereabouts of Marcano's henchmen.
After Lincoln had Sal Marcano and Giorgi Marcano backed into a corner, forcing them to seek refuge in the Paradiso Hotel & Casino, Donovan doused his impromptu surveillance centre in gasoline and set the room on fire to cover up his acts.
He later reconvened with Lincoln and Father James at Saint Jerome's Catholic Church, after Lincoln had finished off the Marcanos, where he advised Lincoln to take over New Bordeaux's criminal underworld and murder his remaining underbosses before they betrayed him. He left the city after this.
While aiding Lincoln with his crusade against the Marcanos, Donovan was also keeping tabs on Connor Aldridge, a former CIA officer who had collaborated with the NVA while in Vietnam and left Donovan for dead. With the help of Robert Marshall, another former CIA officer who now operated as a bounty hunter in New Bordeaux, Donovan identified his involvement in a massacre at a Cuban restaurant in the French Ward.
After interrogating the sole survivor of the massacre, Lincoln and Donovan headed to the C.I.A. Safehouse in Bayou Fantom, where they took out the mercenaries Aldridge hired to keep watch, but were unable to stop him from stealing classified information on a Cuban plane crash, whose cargo was the nuclear warhead of a Russian missile.
Lincoln and Donovan tracked down a survivor of the crash who had settled in Frisco Fields and, rescuing him from Aldridge's mercenaries, ascertained where the plane crashed: an island off the coast of Mexico.
Taking a boat out to the deserted island, which was now overrun by Aldridge's mercenaries, Lincoln and Donovan made their way to the crash site but soon discovered that Aldridge had already made off with the warhead, intent on selling it to one of his contacts in the NVA.
Fighting their way through more of Aldridge's mercenaries, Lincoln and Donovan infiltrated a Soviet bunker on the island, surmising that Aldridge was headed to the submarine bay to take the warhead back to Cuba; wounding Aldridge, who retreated to the submarine, Lincoln waited outside while Donovan confronted Aldridge on-board, killing him with a bullet to the head.
The warhead still intact, Lincoln and Donovan drove the truck carrying it out of the base - having radioed for a helicopter to take the cargo back into the hands of the American government - and, after dealing with the last of the mercenaries, headed back to New Bordeaux.
- See also Mafia III Endings.
In August 1971 John Donovan was called before the U.S. Senate Select Committee on Intelligence to testify about his knowledge and participation in Lincoln Clay's murderous rampage against the Marcano Crime Family.
As the hearings were winding down Donovan asked Senator Blake where he was when John Fitzgerald Kennedy was assassinated. The Senator replies that he doesn't remember, but believes he was at home. Donovan recounts his whereabouts at the time, being in a muddy hut in Vietnam, dismembering an old woman piece by piece because her son was an NVA officer and hurting her was the only way to make him talk.
Senator Blake breaks in, saying he doesn't understand what this has to do..., but he's interrupted as Donovan continues recounting the events of that day, stating that what that NVA officer told him saved the lives of an entire platoon of men. That's 42 men who lived another day because he was willing to take a saw to that old woman. Again, Senator Blake breaks in and stands up as he begins to dismiss Donovan, only to be told by him to sit down and shut up.
Donovan continues by saying he did a lot of terrible things in the name of this country, things that will haunt him for the rest of his life, because he believed this nation stood for. To be sitting ass deep in mud, that old woman scattered all around him, and hearing that the President of the United States had just been murdered, he knew right then and there that he couldn't let that stand and he would make it right no matter how long it took.
Growing impatient, Senator Blake asks Donovan what he's saying, to which he replies that Sal Marcano and a group of conspirators murdered President Kennedy, to which the Senator replies as being the most absurd thing he's ever heard. Assuming he would say that, Donovan pulls out a silenced pistol, aiming it at the Senator. He tells him that he doesn't hold anyone's ambitions against them, and the Senator certainly was ambitious, having gone to law school, become a district attorney, and then a United States senator.
As he approaches the Senator, gun still pointed directly at him, Donovan explains that after Sal died, he went through his files. Imagine his surprise when he saw Senator Blake's name over and over again. The mob wanted President Kennedy dead and Blake was more than willing to help. With the cameras still rolling, and in front of all the witnesses, Donovan states that he wants everyone to know he isn't finishing with Senator Blake, he's starting with him. He then fires one shot into the Senator's chest, followed by another to his head.
Turning toward the camera Donovan states that they're next and waves his gun in front of the other members of the committee. He then laughs as he excuses himself and walks out of the room. What became of John Donovan after that is unknown.
- Donovan drives an orange Potomac Independent, and a blue Bulworth Banyan, which he uses as a mobile tac-center.
- If the player manages to get Donovan killed through an exploit, a special cutscene will play with Jonathan Maguire explaining that after Donovan's passing, Lincoln was unable to wage his war against Sal Marcano and was killed a short time after.