The player takes the role of the protagonist known as Ranger (voiced by Trent Reznor) who was sent into a portal in order to stop an enemy code-named "Quake". The government had been experimenting with teleportation technology and developed a working prototype called a "Slipgate"; the mysterious Quake compromised the Slipgate by connecting it with its own teleportation system, using it to send death squads to the "Human" dimension in order to test the martial capabilities of humanity.
The sole surviving protagonist in "Operation Counterstrike" is Ranger, who must advance, starting each of the four episodes from an overrun human military base, before fighting his way into other dimensions, reaching them via the Slipgate or their otherworld equivalent. After passing through the Slipgate, Ranger's main objective is to collect four magic runes from four dimensions of Quake; these are the key to stopping the enemy later discovered as Shub-Niggurath and ending the invasion of Earth.
The single-player campaign consists of 30 separate levels, or "maps", divided into four episodes (with a total of 26 regular maps and four secret ones), as well as a hub level to select a difficulty setting and episode, and the game's final boss level. Each episode represents individual dimensions that the player can access through magical portals (as opposed to the technological Slipgate) that are discovered over the course of the game. The various realms consist of a number of gothic, medieval, and lava-filled caves and dungeons, with a recurring theme of hellish and satanic imagery reminiscent of Doom (such as pentagrams and images of demons on the walls). The latter is inspired by several dark fantasy influences, most notably that of H. P. Lovecraft. Dimensional Shamblers appear as enemies, the "Spawn" enemies are called "Formless Spawn of Tsathoggua" in the manual, the boss of the first episode is named Chthon, and the main villain is named Shub-Niggurath (though actually resembling a Dark Young). Some levels have Lovecraftian names, such as the Vaults of Zin and The Nameless City. In addition, six levels exclusively designed for multiplayer deathmatch are also included.