Top Gun: Fire at Will is a flight simulator based on the movie of the same name. You take the role of Maverick and must pilot your F-14 Tomcat with your RIO Merlin in the backseat through a series of missions that begin with the Top Gun School in San Diego and continue with conflict zones in Cuba, Korea and Libya. Full motion video cutscenes with live actors play between many of the game's fifty or so missions, with James Tolkan being the only actor to return from the original movie.

The game's overall plot focuses on the player-character, Maverick, going to combat in Cuba, North Korea, and Libya against a secret group of mercenary pilots called the "Cadre."