Flight of the Intruder begins with a night attack mission flown by Jake Grafton and his navigator Morgan "Morg" McPherson from the USN aircraft carrier, USS Shiloh, striking a target in North Vietnam.

Although there are many militarily valuable targets in North Vietnam, Grafton and other aviators are instead routinely ordered to hit worthless targets—typically "suspected truck parks".

Cole, an aggressive veteran with experience over the most heavily defended areas of North Vietnam, becomes aware of Grafton's frustrations, and the two begin to plan an unauthorized mission against a Communist Party center in Hanoi, which will be a serious violation of the restrictive rules of engagement.

Flight of the Intruder, a video game based on the novel, was released for personal computers in 1990 and re-released for the Nintendo Entertainment System around the same time as the film adaptation.

Developed by Rowan Software, Ltd. and published by Spectrum Holobyte, the game allowed players the choice of flying either the A-6 intruder or the F-4 from aircraft carriers against targets in the Democratic Republic of Vietnam.

Eventually, he finds himself serving as an assistant to the Joint Chiefs, and is last heard from in the book The Disciple, working for the CIA (by this time in his late 50s to early 60s).