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.

The Strogg are quickly regrouping. However, with the Strogg’s planetary
defenses still destroyed, Earth's forces can deliver a full and final assault.
This time, you're not alone. You are Matthew Kane, an elite member of Rhino
Squad, and part of Earth’s next invasion wave. An army of soldiers are fighting
with you and an arsenal of weapons and vehicles are at your disposal in this
heroic and epic battle between worlds.