Alpha Mission is a vertical scrolling shooter that has similarities to Xevious, with the use of air-to-air and air-to-ground weapons.

Alpha Mission's storyline is very primitive, as the game was originally designed for Arcade use. The player moves from level to level, fighting off waves of enemies that threaten several different space stations. A boss must be defeated at the end of each level in order for the player to progress to the next level. Power-ups, upgrades, and new weapons can be collected during gameplay, but are all lost when the player dies.