Alpha Mission II is a top-down, vertically-scrolling shooter that follows the legendary Super Jet Plane SYD as it battles to defeat an invading armada and destroy the Fulvalence Groma. The game takes place in 2525, where space is once again under threat.
The gameplay involves picking two armors for the SYD at the start of each level and purchasing additional ones at the end of the levels. Armors add firepower to the ship while equipped and can be destroyed when shot, saving the ship from one hit. The SYD's primary weapons, a straight ahead laser and falling bombs, can also be upgraded using icons dropped by specific enemies.