In some areas of certain stages, the player will fly at a lower altitude armed with only twin machine guns and shooting down parked planes and turrets and can take a limited amount of damage from multiple shots and crashes.

The world order had been restructured as a unitary system; a central supreme government with smaller rebuilt regions of continents as its states.

Then one day, an urgent news reached the headquarter of the central supreme government that its smaller states came under fierce assaults and were occupied by mysterious enemy militaries.

The Group One, an elite air force squad under the central supreme government's command, dispatches two of their ace pilots to destroy the mysterious enemy.

In Japan, Game Machine listed Scramble Spirits on their November 15, 1988 issue as being the second most-successful table arcade unit of the month.