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Assassinating Shub-Niggurath and stopping her invasion of Earth is the main goal of the game. The player fights through the four episodes to locate the four Runes which he/she uses to open a passage to Shub-Niggurath. Shub-Niggurath spawns a force of Shamblers and Vores to kill the player but all fails and the player uses the Spiked Sphere to kill the evil beast and end the threat of Quake.
Shub-Niggurath spawns hundreds evil demons but she has no attacks of her own, relying purely on the power of her children. Shub-Niggurath's one 'combat' ability is her impossible defence. Non of the player's weapons can hurt Shub-Niggurath, making her practically invincible. The only way to kill her is using the Spiked Sphere.
Jumping over to Shub-Niggurath and standing near her will result in the player losing health. This could be some kind of defensive aura.
Shub-Niggurath is confronted in Shub-Niggurath's Pit. To kill Shub-Niggurath, the player must kill a whole load of Shambler and Vore, notable as the most powerful and toughest enemies in the game and reach the far end of the room via a path that goes around her.
At the end of the path, there is a portal which will teleport the player to the location where the Spiked Sphere is currently floating. Watch the sphere and wait for it to fly through Shub-Niggurath. Jump into the portal just as it enters Shub-Niggurath to telefrag her and the game is over. Watch as Shub-Niggurath explodes, revealing the player as the victor.