After they had fought out their civil war on their homeworld called Stroggos, the Strogg ventured out into space to conquer other planets and study other races to integrate them into their own. In 2060 they enter space above their next target: Earth. The Global Defense Force (GDF) is completely overwhelmed by the attack of this highly advanced force but they don't give up and fight for their survival. Ultimately Earth will fall into the hands of the Strogg and the events which lead to the beginning of Quake II will unfold but until then, you'll be an important part of this last battle for control over the planet!
As a successor of Wolfenstein: Enemy Territory, Quake Wars focuses on objective driven gameplay rather than just capturing flags like you do in the Battlefield Series. This means that on every map one team needs to fulfill an objective while the other needs to guard it. For example on the map "Valley" the GDF needs to build a bridge, then drive a MCP over the bridge to a nearby outpost, hack a Strogg-shield so that the MCP can fire a missile into the Strogg base so that the GDF can enter it and destroy a generator.
To make it even more complex, most objectives need to be completed by a specific class. On each side are five classes and each class has special abilities. The engineer for example can build the bridge on Valley, repair damaged vehicles or deploy identities while the Field Ops supports his teammates by handing out weapons and deploying artillery systems. Since the maps are all pretty big, you also have access to several kinds of vehicles ranging from little quadbikes to helicopters.
Unlike most multiplayer games, the teams in Enemy Territory: Quake Wars don't just have a different skin but are actually completely asymmetrical balanced from classes over weapons to vehicles. This means that while both teams have a medic, they both function differently. The GDF medic for example behaves like every other medic by instant reviving his teammates but the Strogg technician needs a few seconds before his dead companion is alive again. To balance this out, the Strogg technician can turn dead GDF soldiers into spawn hosts. So if he dies, he respawns at such a host (if it hasn't been destroyed).