Ultimate Air Combat has 36 different missions, then one last final mission. Each mission is grouped into two parts. The first part uses a cockpit view where the player must shoot down three planes before either running out of fuel or getting shot down by enemy planes. After that, the second half of the mission uses an isometric view where the player must destroy enemy forces and installations.

The story begins when the White House calls an emergency meeting, where they reveal that the military dictator Don Gwano is using the high revenue from his large oil exports to fund his large army and navy. He is now attacking neighbouring countries and the president's military advisers have agreed that action needs to be taken. Rather than a full-scale invasion, they propose a tactic of quick lightning strikes to take out specific systems vital to Don Gwano's militaristic regime. As the top pilot in the military, the player is chosen to perform these attacks.