Story
"Raiden is about to be killed by Shao Kahn, and just before he delivers the last blow, Raiden sends a mental message to his earlier self by saying that he must win, and the camera rewinds back to Mortal Kombat 1. The Raiden from Mortal Kombat 1 then gets the message and experiences a premonition. The game then spans Mortal Kombat 1, 2, and 3, retelling the story with an enlightened Raiden, who has changed the course of events. Eventually, everything the player has seen happen before — Liu Kang winning, Lin Kuei turning into cybernetic ninjas, has been altered. You might see a cybernetic character who wasn't before, and a different version of events.During the events of the first tournament hosted by Shang Tsung, the past version of Raiden sees visions of the future courtesy of a now cracked amulet. Raiden initially comes to the conclusion that fighter Liu Kang is to win the tournament and save Earthrealm from Outworld. Pivotal characters such as Johnny Cage, Sonya Blade, Jax Briggs, Sektor, Cyrax, Nightwolf, Kitana, Jade, and Sub-Zero are introduced, the latter being murdered by the hellspawn Scorpion. In time, Liu Kang remains the only Earthrealm champion, and succeeds in defeating Shang Tsung and the Shokan Prince Goro. However, Raiden's amulet continues to deteriorate, a sign that future events remain unchanged. Disappointed with Shang Tsung's failure, Shao Kahn orders his execution, but relents when the sorcerer suggests holding the second tournament in Outworld. Raiden initially refuses, but is forced to relent when Shang Tsung threatens to unleash Outworld's armies upon Earthrealm.
As each of the Earthrealm warriors are defeated, the younger Sub-Zero (originally named Tundra, who adopts the moniker Sub-Zero to honor his fallen brother) and Smoke arrive in Outworld on Lin Kuei terms, who are also fighting in the tournament. They are pursued by cybernetic Lin Kuei assassins, including Sektor and Cyrax, who attempt to take them back to Earthrealm for automation. Raiden attempts to change the timeline by rescuing Smoke from his transformation, but as a result, the younger Sub-Zero is automated in his place. Also during this time, Kitana uncovers the existence of Mileena, a mutant clone of herself crafted by Shang Tsung on Shao Kahn's orders. Infuriated by the betrayal, Kitana defects from her father and joins the Earthrealm warriors. In the final round of the tournament, Raiden once again tampers with the timeline by substituting Kung Lao for Liu Kang, the original winner of the Outworld tournament, as the champion of the second tournament. Shao Kahn, however, kills Kung Lao from behind, with Liu Kang retaliating and mortally wounding the villain. Raiden notes the timeline is still unaffected as his amulet continues to deteriorate.
Healed by the sorcerer Quan Chi, Kahn enters into an alliance with the Netherrealm and resurrects his wife, Sindel. In doing so, they nullify the ward that prevents Kahn's access to Earthrealm, initiating a full-scale invasion. Shortly afterwards, Raiden prevents the murder of Johnny Cage by slaying Motaro. Joined by fighters Kurtis Stryker and Kabal, the Earthrealmers attempt to stop Kahn, although many of them are murdered by Sindel, who had been vastly empowered by the souls extracted from Shang Tsung's body, thus killing the sorcerer. Nightwolf, however, sacrifices himself to kill Sindel. Raiden confronts Quan Chi and, learning of the alliance with Kahn, he realizes that the message "He must win" refers to Kahn himself — if he is allowed to merge Outworld and Earthrealm, he will be punished by the Elder Gods for a violation of the Mortal Kombat code for taking a realm without winning the tournament. Liu Kang, however, blames Raiden for the death of their allies and attacks an approaching Shao Kahn. In an attempt to change history, Raiden accidentally kills Liu Kang. Grief-stricken, Raiden "surrenders" to Shao Kahn. The Elder Gods intervene, restoring Raiden's strength which he in turn uses to defeat and punish Kahn for breaking the Mortal Kombat code.