The story of A/X-101 takes place in the year 2500, where humanity is under attack by the alien Gurzons. The Earth Defense Force is no match for the enemy, and cities are destroyed across the planet. However, a chance to turn the tide comes when enemies from the planet Prism offer their help. With the ultimate weapon, the A/X-101 system, a few EDF pilots might be able to make it to Prism and change the course of the war.
The gameplay in A/X-101 is an on-rails shooter, with players controlling one of four starfighters as they move through pre-rendered space and planetary environments. The player's ship moves automatically, but only the targeting crosshair can be moved freely to hit enemies. Two types of projectiles are available: Laser Cannons, which have unlimited ammunition but take time to recharge, and Fusion Warheads, which function as smart bombs but are limited in supply.
Between shooting levels, there are transitional cutscenes that pre-render the player's journey through space. The game features a unique blend of action and strategy, requiring players to make the most of their limited resources to succeed.