An evil alien named Hood wants the Thunderbirds to turn over all their vehicles to him within a 60 day time period or Hood will bombard the Earth with meteors. The Thunderbirds figure he needs the 60 days to prepare to come through with his threat so they decide to go looking for places which may contain his energy sources for his power.

The game takes place over North America, the Indian Ocean, and Asia as you fly through doing different missions in each location. As a Thunderbird, you'll fly 5 different futuristic aircraft such as a Mach 20 Thunderbird 1 Rocket, the Neptune Hydro-Turbojet, and the Fire Flash Atomic plane. Each vehicle can only take 3 hits before being grounded. If your vehicle is grounded, it will take 3 days to be repaired. These 3 days will be subtracted from your overall 60 days you have to beat the entire game.

Your enemies consists of such exotic fare as poisonous space scorpions, mutant sea worms and even environmental adversaries such as fire spitting volcanoes. By defeating certain enemies, you aircraft can gain powerups such as replenishing depleted heath, increased firepower, or adding orbital ships to fly by the side of your main ship to assist you in combat.