WMG: Quake

Quake 1 is part of the same continuity as Quake 2 and 4
More specifically, Quake 1 is set centuries before 2 and 4. Back then, the Strogg were just a race of Human Aliens who did not yet enhance their bodies with bionics, nor did they form a Hive Mind. In Quake 1 you play as a Strogg: this can be inferred from the Strogg symbol on the military crates you see throughout the allied bases.

The story of the game involves Lovecraftian creatures, led by Shub-Niggurath, coming through "slipgates" (teleporters or portals) to invade this dimension. Evidently, the whole experience was so shocking for the Strogg, they decided to research bionics in order to turn themselves into superior beings and repel eventual future invasions more easily. In time, this got out of hand, and bionic enhancements became an end onto itself, instead of a means to reach an end. Alternatively, Sub-Niggurath's influence may have subtley corrupted the Strogg, leading them to take their research too far.

Ever notice the military crates in Quake 1? They have the Strogg symbol on them. This means that in Quake 1, the "good guys" are Strogg! And, more specifically, Quake 1 is set centuries before 2 and 3, when the Strogg were simply a human-like race, without any experience in bionic implants yet.
  • To some extent, it can be argued that every game is connected in some way or another. The Quake timeline may as well could be Quake I-[ET Quake Wars-Quake II-Quake IV]-Quake III Arena.

Building on this, in Quake, the humans are researching Slipgate technology. What did the Strogg use to attack Earth in Quake Wars? Slipgates. Ho hum.

All Strogg are let by a brain damaged computer that started improvising spare parts
Originally designed to destroy the enemies of the alien race that became the Strogg the computer started cannibalising its enemies, its dead and finally its own people in order to 'win the war'. A war that ended hundred of years ago, is still being fought by a insane program that is now harvesting other worlds to re-establish its strength to keep its home world safe. Somewhere along the line it started to forget how to use and develop certain technologies, leading it to use genetic engineering and body parts to create replacement parts. Some of the original Strogg race still exist, in stasis, waiting for the computer to tell them its safe to wake up.

The events of Quake 1 were orchestrated by the Vadrigar
Unlike the forces of Hell or the Strogg, Shub-Niggurath and her forces only appear in one stand-alone game. Since the Vadrigar are apparently capable of abducting fighters across time, space and even dimensional barriers, it's reasonable to assume that creating their own race of beings would be child's-play. So the Vadrigar created Shub-Nigurrath and her forces and then waited for mankind to stumble upon them, anticipating that Ranger or somebody similar would succeed in destroying Shub-Niggurath. At the end of the game, the Vadrigar are left with a warrior accustomed to interdimensional travel and fighting supernatural foes like those that appear in the Arena Eternal.