Set in Vietnam, during Operation Linebacker in 1972, Flight of the Intruder lets the player pilot the F-4 Phantom II and A-6 Intruder through 13 campaign missions, or take the role of an Air Group Commander with the ability to create (and fly) their own missions. The missions are played alongside up to 7 AI wing men (4 of each aircraft type), and the player can switch between the planes at will, as well as select their loadouts in the pre-mission briefing. At the games harder difficulty levels the the player would have to worry about the reliability of the plane and it's weaponry - the F-4 would not have an internal cannon, and would have to rely on heat seeking and radar guided missiles that were prone to misfire, as well as an engine creating a visible smoke trail that would alert enemies. On the hardest difficulty the player would also have to follow basic rules of engagement. There were - as per usual for flight simulators at the time - several difficulty levels and an easily accessible cheat menu that would allow the player to make the plane invincible or have unlimited ammunition.
There was a non-advertised serial port based multi-player mode included in the game, where one player would be able to fly the MiG's (otherwise not accessible to the player) in head to head combat.
The game was in production before the novel's publication. Mirrorsoft obtained permission to use Coonts' name after the novel was a success, and the book was bundled with most releases of the game. He also wrote the introduction to the manual.
Rereleases after 1991 generally used the same cover art as the movie.