The evil Outworld emperor Shao Kahn opens a portal to Earthrealm (Earth) and has resurrected his queen Sindel, Princess Kitana‘s long-deceased mother. Earthrealm is therefore in danger of being absorbed into Outworld within six days, a fate which reigning Mortal Kombat champion Liu Kang and the other Earthrealm heroes must fight to prevent. When Kahn kills Johnny Cage during a confrontation with the thunder god and Earthrealm protector Raiden (spelled Rayden in the film), he and the remaining Earthrealm warriors must regroup and find a way to defeat Shao Kahn. An emotionally distraught Sonya Blade enlists the help of her Special Forces partner, Jax. Together they destroy the robotic ninja Cyrax, later in a ensuing fight Sonya kills Mileena. Kitana and Liu search for a Native American shaman named Nightwolf, who seemingly knows the key to defeating Kahn. Kitana and Liu destroy another robotic ninja Smoke with the aid of Sub-Zero (the younger brother of the one seen in the original film), but Scorpion suddenly appears, attacks Sub-Zero, and kidnaps Kitana.
Meanwhile, Rayden meets with the Elder Gods and asks them why Kahn was allowed to break the tournament rules and force his way into Earthrealm, and how he can be stopped. The answers he receives are sparse and ambiguous; one says that reuniting Kitana with her mother, Sindel, is the key to breaking Kahn’s hold on Earthrealm, but another Elder God insists that the defeat of Kahn himself is the solution. Rayden is then asked by the Elder Gods about his feelings and obligations towards the mortals, and what he would be willing to do to ensure their survival. Liu finds Nightwolf, who teaches him about the power of the Animality, a form of shapeshifting which utilizes the caster’s strengths and abilities. To achieve the mindset needed to acquire this power, Liu must pass his tests. The first is a trial of his self-esteem and focus. The second comes in the form of temptation, which manifests itself in the form of Jade, a mysterious warrior who attempts to seduce Liu and offers her assistance after he resists her advances. Liu accepts Jade’s offer and takes her with him to the Elder Gods’ temple, where he and his friends are to meet Rayden. The third test is never revealed.
At the temple, the Earthrealm warriors reunite with a newly shorn Rayden, who reveals that he has sacrificed his immortality to freely fight alongside them. Together, they head for Outworld to rescue Kitana and reunite her with the undead Sindel in hopes of restoring her soul and closing the Outworld portal to Earth. With Jade’s help, Liu rescues Kitana, while the others find Sindel. However, Sindel remains under Kahn’s control and escapes during an ambush, while Jade reveals herself to be a double agent sent by Kahn to disrupt the heroes’ plans before he feeds Jade to a gargoyle for her failure. Rayden then reveals that Shao Kahn is his brother, and that the former Elder God Shinnok is their father. He realizes that Shinnok had lied to him and is supporting Kahn. With renewed purpose, Rayden and the Earthrealm warriors make their way to the final showdown with Kahn and his remaining generals Motaro and Ermac, along with Sindel. Shinnok demands that Rayden submit to him and restore their broken family, at the expense of his mortal friends. Rayden refuses and is killed by an energy blast from Shao Kahn. After a hard fight, Jax, Sonya, and Kitana emerge victorious over Kahn’s generals, but Liu struggles with Kahn, and his Animality barely proves effective, exposing a cut to Kahn that proves he is now mortal. Shinnok, who explains that these are the consequences for breaking the sacred rules, attempts to intervene and kill Liu on Kahn’s behalf, but two of the Elder Gods arrive, having uncovered Shinnok’s treachery. They declare that the fate of Earth shall be decided in Mortal Kombat. Liu finally defeats Kahn, and Shinnok is banished to the Netherrealm. Earthrealm reverts to its former state and with Kahn’s hold over Sindel finally broken, she reunites with Kitana. Rayden is revived by the other Elder Gods, who bestow upon him his father’s former position. With everything right in the universe once again, the Earthrealm warriors return home.