The Earthrealm heroes must journey to Outworld and fight for the survival of their homeland, invaded by the forces of evil warlord Shao Kahn, in the tournament to end all tournaments: the final Mortal Kombat.
The movie picks up right after Scorpion's Revenge where the heroes are attacked by Shao Kahn, which will force "Raiden and his group of warriors into a deal to compete in a final Mortal Kombat that will determine the fate of the realms." This forces the good guys to travel to Outworld defend Earthrealm while Scorpion journeys to find the Kamidogu (a mystic relic made by the almighty Elder Gods) before it is used to bring back the mysterious One Being, who would destroy the universe.
After the events of the first Mortal Kombat tournament Liu Kang, Raiden, Johnny Cage, Sonya Blade and Jax Briggs return home to find EarthRealm has been invaded by the forces of Outworld. The evil warlord Shao Kahn presents our heroes with an ultimatum; agree to a new Mortal Kombat tournament or face an all-out war with Outworld. Now our heroes, along with new allies Kung Lao and Stryker, must journey to Outworld and fight for the survival of Earthrealm in the tournament to end all tournaments; The final Mortal Kombat.
Shao Kahn launches a new Mortal Kombat tournament in Outworld after the events of the previous one, declaring war on Earthrealm in retaliation for Shang Tsung's loss. Kung Lao, Jackson Briggs, who has been cybernetics enhanced by Special Forces, and NYPD officer Kurtis Stryker repel the Emperor's first wave invasion force of Outworld warriors and Netherrealm demons, which includes Princess Kitana, Kintaro, General Reiko, and Jade. Jax's partner Sonya Blade and movie star Johnny Cage confront the Outworld commanders at the beginning of their attack.
After negotiations break down and Liu Kang and Raiden join Johnny and Sonya, Shao Kahn shows up and asks Raiden to take part in a final Mortal Kombat tournament in order to permanently determine Earthrealm's destiny. After receiving approval from the thunder god, he and Shao Kahn travel to the world of the Elder Gods to suggest this final competition.
In the meantime, Scorpion returns to the Netherrealm and reawakens. The Elder God Shinnok, who is furious about the passing of his favorite servant Quan Chi, confronts him. In order to use the key embedded in Scorpion's body to find the last piece of his puzzle, the Netherrealm lord plans his entrance into Earthrealm. He then hires the Lin Kuei clan to track him down and retrieve his prize in an anonymous manner. The grand master calls on Kuai Liang and Smoke, two members of Lin Kuei, to assist with the request back in Earthrealm. However, they are appalled to see that peers they would have doubted were missing before their requested presence had undergone cybernetic modifications to fortify the clan, and the juniors are expected to follow suit. Both Liang and Smoke rebel, but only Liang manages to escape. Sub-Zero, the code name of his late brother, is then adopted by Liang.
Raiden arranges to host and take part in the tournament while giving up his immortality, and then he returns to his troops at the Wu Shi Temple. After the Earthrealm warriors depart for Outworld, Raiden is informed of Scorpion's presence. He says that the key to Shinnok's prison has become a part of his soul and that he sought Raiden's counsel regarding its function. According to Raiden, it is the Kamidogu, a supreme magical relic from a bygone era that holds the key to untold power and has the potential to end all realms.
The tournament begins with the Kytinn warrior D'Vorah defeating Cage; Sonya defeating D'Vorah and Li Mei; Kang defeating Jade; Stryker defeating Baraka; and Jax tearing his arms out of their sockets to defeat Kintaro.
Back on Earth, Cyrax and Sektor are pursuing Scorpion in a shipping yard by the dock. Sub-Zero quickly interrupts the trio, but even he is surpassed by their superior enhancements and the cybernetic Smoke's appearance. The three cyber Lin Kuei capture their Hellspawn prey and flee to the Temple of Elements, their adversaries overpowered. When they arrive at their destination, they make Hanzo open their assigned portal. When they reach its gateway and are about to kill him, a resentful Sub-Zero interrupts them once more. Scorpion accepts a short-term alliance against Sub-Zero's clan but is unable to comfort Kuai Liang over unintentionally killing his brother. The Lin Kuei manage to recover the Kamidogu in spite of their efforts, but the mountain collapses on top of them, leaving the two dead.
Shao Kahn and Shang Tsung kill Lao and Stryker, respectively, as the second half of the final tournament begins. Instead of battling Raiden, Kitana rebels against her stepfather, only to be subdued by beatings. Kang spares Shang Tsung and defeats him despite any setbacks.
The Lin Kuei discover Shinnok's scheme to resurrect the One Being and end creation in the Netherrealm, but they discover too late that Shinnok was their employer. They are then betrayed and killed in exchange for their services.
When Raiden loses his fight with Shao Kahn in the tournament's last round, Kang becomes enraged and defeats the emperor to win the title. Celebrations are short-lived, though, as Shinnok eventually manages to fuse himself and bring the One Being back to life. Johnny, Jax, Kitana, and Sonya defend civilians from Kahn's remaining army, while Sub-Zero, Scorpion, and Liu Kang fight and kill Shinnok with the Elder Gods' help.
Later, Kang absorbs the power of the One Being and restores Edenia and the other realms to their native states. In hard-won tranquility, Liu and Kitana hold hands without realizing that Raiden's immortality has brought him back to life, while Sonya and Johnny kiss.
