WMG / Quake

Ranger is a Strogg without implants.

And here is the evidence.

• In Quake 1, the emblem of Ranger's military organization is a skull with stylized wings. In Quake 2 and 4, the same emblem represents the Strogg.
• Ranger is counterattacking an invasion of Lovecraftian monsters who come from a military teleportation device called Slipgate. In Enemy Territory: Quake Wars, the Slipgate is Strogg technology.
• In Quake Wars, the Slipgates are shaped like a Quake 1 symbol.

This universe is the same one where the Strogg exist, but Quake IV's re-imagining of the universe especially ties in to this game.

Notably, the Strogg were able to develop their own [Super]-Nailgun and variant of the Thunderbolt and as mentioned above, the Strogg even have possession of Slipgate technology. The lack of the Quad Damage in the single-player campaign is a consequence of the Stroggs' lack of knowledge about recreating the magic in this artifacts; they're probably captured and hidden away where they are never seen because the Strogg are attempting to reverse engineer them. On the other hand, the Strogg research into Dark Matter lead to major developments and may even be related to the Slipgate technology.

Cell ammo is powered by stolen magic energy.

At first glance, the seeming incongruities of the Cell weapons are a bit confusing: even though they come in very high-tech looking boxes and are only dropped by the futuristic Enforcers, two of the weapons that they provide ammo for - the Thunderbolt and the Mjolnr - both have a very magical, arcane appearance, and can only be acquired in the more fantastical levels. These squares can be circled when we consider the ubiquitous presence of the crates scattered about both sides of every level with Slipgates: clearly, the army of Grunts and Enforcers are collecting *something* from the other dimension, and are carrying it back home with them. Considering how Ranger is not able to use the Enforcer’s laser rifle (and only acquires the laser cannon after the end of his first adventure), it stands to reason that they have access to some kind of secret power source, never before seen on Earth. Consider also that “The Wizard’s Manse”, where the Thunderbolt is first found, has clearly been long abandoned by the titular wizard: its floors have caved in to let the swamp water and slime overtake them, it’s devoid of furniture or any other signs of habitation, and some of the walls and doorways have been defaced by vandals. Who’s to say that Quake’s humanoid army from Ranger’s dimension didn’t stumble upon the decrepit house and help themselves to what they found inside?

Shub-Niggurath isn’t truly dead

Do you really think an all-powerful Outer God who ruled across four whole dimensions could be destroyed just with a telefrag? Instead, Ranger didn’t kill her, he only destroyed her physical manifestation. This also explains how the monsters keep coming around after she’s “dead” and who’s leading them after Armagon has been killed.

Knights and Death Knights aren't human, they're orcs.

We've got ogres, and another expansion adds goblins. Probably the most humanlike creatures that worship Quake other than her actual human followers would be Orcs that use dark sorcery to create slipgates.