Silpheed for the Sega Mega CD is a shoot-'em-up game that follows a similar gameplay style as its PC counterpart. The player controls a ship moving in a 2D plane that extends into the screen, reminiscent of a pinball table. The Sega CD version features pre-rendered video backdrops and polygon graphics for the player ship and enemies.
The story revolves around a central computer system being hacked by terrorists who are using it to attack colony planets throughout the galaxy. The Galaxy Union's last hope is the player, who must fight their way through 11 stages to reach Earth and reclaim control of the computer.