A long war has ended and the Galactic Empire has grown but it isn't stable. Rebel groups still fight the regime but with the invention of genetic transformation, a normal civilian can be transformed into a mindless, easy to command but strong fighting unit. These civilians weren't asked, they were forced to undergo the procedure. You play one of these civilians. First they took your daughter and then they came for you. But before the procedure was completed, you were rescued by the rebels. Now it's your turn to fight back.

Gene Troopers is basically a shooter but it lets you build and upgrade your weapons with stuff you find lying around. You can also extract the genes of an enemy to upgrade your own. With these codes you can choose in which direction you want to go with your character. This means you can either choose to upgrade your stealth abilities or to devote them to becoming a fighter.

The game takes you to 6 different planets including a jungle world. There are drivable vehicles and team members to help you with your task.