A young hero is running back to his loved ones, only to see the city nuked and his loved ones lost. Hellbent on revenge, he climbs into his ship to find out where the terrorists are hiding. With only a clue from a fellow pilot, he's now on his own. Following the clues, they seem to lead to Greenland, some islands and Egypt, eventually leading to Italy. Equipped with lasers, bombs and heat-seeking missiles it's time for the terrorists to get a taste of their own medicine.

Zone 66 is a top-down shoot 'em up where the goal is to take out enemy installations and ships on each island. When starting a mission you can select which of the 9 different ships to pilot before taking off from your own base. In order to advance you need to take out all main ground targets to complete a mission. Targets are indicated on the ship's radar, and you can re-spawn as many times as you like, provided that your base still has supply bays standing. The story advances as each mission is beat, provided that no cheats have been enabled.