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.
As you shoot your way through all the enemies with 50 different weapons from normal pistols to powerful energy weapons, you gain experience points and level up. At each level-up you are awarded some skill points with which you can improve your character in several areas like fighting better with pistols or investing it in strength so you can carry more items in your inventory.
You can also find and buy items like med packs or install implants like a booster which makes you nearly invulnerable for a short period.
Once you've finished the campaign you can either jump into the survival mode, in which you have to fight wave after wave of aliens or play with a friend in LAN in several modes from normal deathmatch to a coop-survival-campaign.