The year is 2161 and the aliens try once again to invade Earth. You are a mercenary of the M.A.G.M.A Corporation that is sent in to help the US Army get rid of the plague. So under the command of General Baker you take on missions and kill many thousands of aliens on your way.
As in the predecessor Alien Shooter, you control your character through 2D isometric maps to find key-cards, activate machines and clear areas from the aliens. At the beginning you have the choice between 8 characters who have different skills. There's everything from a sniper to a hands-on melee fighter. You also choose one of eight special talents like self-heal or night-vision.