Earth is under siege by an alien race. The Strogg are cybernetic warriors--a mechanical frame and decaying body parts stabilized by flesh consumed in a systematic annihilation of other species and civilizations. In a desperate attempt to survive a Strogg attack on Earth, an armada of Earth's finest warriors is sent to take the battle to the Strogg home planet. Earth's initial assault force is nearly annihilated immediately, but one marine manages to infiltrate the base, bring down their planetary defense systems, and kill the Strogg's collective brain and leader--the Makron. Earth assumed the destruction of the Makron would end it all, but it didn't. That's where QUAKE II leaves off and QUAKE 4 begins.