Shao Kahn has won. The Earthrealm is no more. In order to revive his Queen Sindel, the emperor Shao Kahn used the Outworld Tournament from Mortal Kombat 2 as a diversion while his Shadow Priests revive his fallen Queen on Earth. Once enacted, the dimensional bridge between the two realms connects, allowing Kahn's extermination squads to invade and destroy Earth, and enslave the population's souls.
A small team of Raiden's "Chosen Warriors" survives the attack: Mortal Kombat champion Liu Kang and his ally Kung Lao, Special Forces agents Sonya Blade and Jax, the shaman Nightwolf, the riot cop Stryker, the nomadic Kabal, and former Lin Kuei warrior Sub-Zero, who has gone rogue from his clan. Facing the warriors are the mercenary Kano, cyber-ninjas Smoke, Sektor and Cyrax, Sheeva, a female Shokan, the sorcerer Shang Tsung, and Queen Sindel herself.