The year is 2020, and global depression has descended upon the societies of the Earth. When humans least expect it, aliens from a mechanical planetoid attack seemingly without any reason. The League of Nations collaborates with NASA to produce a powerful space fighter under project name Aldynes. When a pilot known as Fox-A is killed, his girlfriend Hiroko heads to the air base where works on Project Aldynes took place. As the aliens launch their attack, Hiroko hijacks one of the fighters and enters the battle.
Aldynes is a horizontally-scrolling sci-fi shoot-em-up. Player-controlled spaceship can acquire power-ups that either change its default vulcan gun to lasers that shoot either straight ahead or in different directions, or enhance the shot of an already equipped weapon. A special power-up adds a small ship that fights alongside the player-controlled one; collecting more power-ups of the same kind adds more ships. These ships can be ordered to stay behind and repeat the shooting patterns of the player-controlled craft, or shoot at enemies following their own AI.
The player-controlled fighter does not have hit points and loses a life every time it is hit. There are seven stages altogether, each ending with a massive boss battle.