- "After defeating Shub-Niggurath, you arrive back at your home base on Earth, but it's not all blue skies and butterflies. Apparently, not all QUAKE forces have been subdued. Chaos ensues as you blast your way through the QUAKE minions and toward the infested gateway. Your only choice is to find the source of evil and shut it down. Without any hesitation, and with more guts than common sense, you leap into a portal of unknown destination."
- — id Software overview
Main Article: Quake Mission Pack 1: Scourge of Armagon Story
After the protagonist defeats Shub-Niggurath, he returns home to find Armagon has taken over Quake's Forces and plans on destroying Earth using the Rift. Therefore, the hero must once again venture into the dark realms of Quake and defeat the armies of evil.
Unlike Quake, where each episode began with a human military base map, Scourge of Armagon has three episodes and the entire first episode is made up of military-style levels on Earth. To compensate for traditional selection of human base map enemies in the game, namely the Grunt, Rottweiler and Enforcer (some of the weakest enemies in the game) and avoiding a whole episode of weak enemies, a new enemy has been introduced: the Centroid.
- Command HQ (difficulty selection)
- The Centroid is a man-sized cybernetic scorpion with nailguns for claws and melee sting attack. Appears mainly in human base maps, but also in the demon world maps. Also known as the Scourge.
- The Gremlin is a humanoid which can jump at the player and steal his active weapon.
- The Spike Mine is a floating ball of what appears to be flesh, approximately a meter across. Covered in numerous spikes. Slowly drifts towards the player (often from behind or from dark areas) and detonates with a powerful explosion when close enough.
- Armagon is the Final Boss of the game and leader of Quake's forces after Shub-Niggurath is killed.
- The Mjolnir is a large hammer which emits lightning on impact with a solid surface (provided the players has enough cells), or alternatively a simple melee weapon. Evidently inspired by the hammer of Thor from Norse mythology.
- The Laser Cannon is a rapid fire energy weapon firing red energy bolts.
- The Proximity Mine Launcher fires grenades that attach to walls or other solid surfaces (though not monsters). They will not detonate until enemies or a player moves too close to them. As such they allow some degree of tactical play.
- A new soundtrack with a somewhat different music style - combination of ambient, metal, and orchestral music.
The game received yet another favorable review. Gamerankings rank the game 82.00%. Despite, the criticizing of only expended the game-play. 
|Quake: The Scourge of Armagon|
|Enemies||Centroid · Death Knight · Enforcer · Fiend · Gremlin · Knight · Ogre · Rotfish · Rottweiler · Scrag · Shambler · Spawn · Spike Mine · Vore · Zombie|
|Weapons||Axe · Grenade Launcher · Laser Cannon · Lightning Gun · Mjolnir · Nailgun · Super Nailgun · Proximity Mine Launcher · Rocket Launcher · Shotgun · Super Shotgun|
|Powerups||Green Armor · Yellow Armor · Red Armor · Biosuit · Megahealth · Pentagram of Protection · Quad Damage · Ring of Shadows|
|Expansions of Quake|
|Quake||Scourge of Armagon · Dissolution of Eternity|
|Quake II||The Reckoning · Ground Zero|
|Quake III||Team Arena|