The Germinator is a futuristic shoot-em-up where players control Norton, the Germinator. Inside his craft, he needs to stop viruses, trojans and worms within the PC Norton has been installed on. Using cel shaded graphics players command the ship through different tunnels, shooting swarms of viruses. Movement and shooting is controlled through the mouse, while three keys change the ship and its bullets into three different colours: red, green and blue. This need to be done to adapt to the colour of approaching enemies. Every enemy can be killed regardless of the colour of the bullets, but by using the correct ones twice as much damage is done. Consecutive hits with the correct colours lead to higher scores. Players can also collect power-ups such as double or triple bullets, extra lives, a shield or a smart bomb. Smart bombs are activated through the right mouse button and clear the entire screen.
The game starts with five lives and a score is kept based on the performance. In later levels, more enemies appear, shooting spiked bombs, the swarms become more dense and enemies in magenta and purple appear. These can be hit on maximum damage by combining any of the two colours they are composed of.