Major Jackson "Jax" Briggs and Lt. Sonya Blade returned to the US and reported these recent events to the American government. After supplying them with details on Kahn's plans, the two were considered insane. They were left with no choice but to prepare independently for the invasion. Jax equipped himself with bionic arms.

Liu Kang returned to the Earth realm with Johnny Cage and Kung Lao, as they prepared to take on the forces of Outworld.

Sub-Zero and Smoke returned to Lin Kuei headquarters and found that members of the clan were being automated. The Lin Kuei were building cybernetic ninjas to take the place of human services, the first two being Cyrax (Unit LK-4D4) and Sektor (Unit LK-9T9). Sub-Zero and Smoke refused to be automated, so they tried to escape. Sub-Zero succeeded in doing so, but Smoke was captured by the clan and was turned into a heartless cybernetic assassin with only a fraction of his true self left in him. Sub-Zero went on to prepare for the invasion. He removed his mask to signify his quitting Lin Kuei, and he joined the rebellion against Shao Kahn's forces. The Lin Kuei then sent Cyrax and Sektor to assassinate Sub-Zero.

Kano, having escaped capture from the US Army, remained in the Outworld and made a deal with Shao Kahn. He would teach the emperor's forces to use Earth weapons, in exchange for his life. Sheeva, a female member of the Shokan race, was appointed as Sindel's personal protector. Motaro, a Centaur (a race that opposes the Shokan by nature), was assigned to lead the attack on Earth. Sheeva grew suspicious of Kahn's loyalty to her race. Shang Tsung remained in the position of Kahn's lead sorcerer.

The Invasion
A large portal opened in the sky and panic filled the streets. The elder gods chose a lineup of Earth's warriors and protected their souls, but not their lives, from Kahn. Shao Kahn entered the Earth realm, merged it with the Outworld, and took the souls of Earth's inhabitants, slowly turning Earth into a part of the Outworld. Knowing that the chosen warriors would survive, Kahn sent out extermination squads led by Motaro to eliminate the survivors. Johnny Cage was one of their many victims.

After the attacks of the extermination squads, only eight chosen warriors remained: Sub-Zero, Jax Briggs, Sonya Blade, Liu Kang, Kung Lao, and three fighters who were not involved prior to the invasion, Curtis Stryker, Kabal, and Nightwolf. Curtis Stryker was an American riot cop who worked the night of the invasion. Kabal, once a member of the Black Dragon organization, suffered severe beatings by the extermination squads, surviving only with the aid of an artificial respirator. Nightwolf was a Native American historian, and preserver of his people's traditions. He used the magic of his shaman to protect his tribe's sacred land during the invasion.