Some time after Shinnok's defeat at the hands of Cassie Cage, Raiden is seen torturing the fallen Elder God in the damaged Jinsei Chamber. The God of Thunder, now with a darker persona due to the Jinsei's corruption, announces to Shinnok that he will no longer have mercy and will destroy Earthrealm's enemies before they can attack the realm. Dark Raiden threatens him, saying that he will be the first. Shinnok reminds him that he can't kill an Elder God. Dark Raiden, preparing his thunder blade, replies by telling him, "There are fates worse than death." After this, Raiden decapitates Shinnok, and informs the severed, yet still-living, head of Shinnok that he will deliver him to Liu Kang in the Netherrealm as a warning, and teleports away.The Keeper of Time, Kronika, appears in the chamber, annoyed at Raiden for upsetting the balance of time after Mortal Kombat X’s events. She approaches and tells Shinnok that the arc of the universe bends at her will, and that it is only a matter of time.Tired of Earthrealm’s defiance, Kronika will bring order to the universe through any means necessary.
After Kronika's defeat, Fire God Liu Kang is about to restart and reshape history, with mortal Raiden's guidance. However, he is suddenly interrupted by the appearance of Shang Tsung, Fujin and Nightwolf. Before the events of the time-merger, they had been imprisoned by Kronika in the Void, unable to do anything but watch the events unfold. With Kronika's death, they were released from the Void, and have traveled through the Hourglass to stop Fire God Liu Kang from using it. Shang Tsung explains that without Kronika's crown (which was unknowingly destroyed by Fire God Liu Kang), using the Hourglass would destroy all realms. Fire God Liu Kang suggests going back in time and defeat Kronika a different way, thereby gaining the Crown, but Shang Tsung points out that plan would be too risky and would not be guaranteed. He instead suggests that he be sent back into the past to regain the Crown at his island. Mortal Raiden does not trust Shang Tsung, and although Fire God Liu Kang shares his sentiment, it is agreed to go with Shang Tsung's plan. Fujin and Nightwolf are sent along with Shang Tsung to watch over him for any signs of betrayal.
Meanwhile, Kotal Kahn has the imprisoned Kollector brought into the middle of the Outworld coliseum for execution, for "escaping Kotal's justice and sucking dry the bounty of Outworld's people". Kollector warns Kotal that his death will cause him to lose. Kotal, who denies being like Shao Kahn, refuses to "inflict a bandit upon the poor". But just before he can execute Kollector, Kronika begins changing time, causing timequakes in the present.
Johnny, Cassie, and Jacqui encounter younger versions of Johnny, Sonya, and Jax, while Dark Raiden is erased from existence, leaving behind Shinnok's amulet.
During the Outworld timequake, Kollector breaks free from his bondage and, along with Kotal, encounters younger versions of Skarlet, Erron Black, Baraka, Kano, Shao Kahn, Liu Kang, Kitana, Kung Lao, Jade, and Raiden. Shao Kahn is surprised that Kotal has become Kahn of Outworld, to which Kotal explains he became Kahn by right after Mileena's and Shao Kahn's deaths. Raiden explains to Kotal that Kung Lao had just defeated Quan Chi and Shang Tsung, which Kotal reveals to the Thunder God happened over 27 years ago. Raiden deduces that the past and present are colliding, while Kotal reunites with his lover, Jade. Shao Kahn's forces engage in kombat with Raiden's and Kotal's forces to reclaim the Outworld throne. After Kotal defeats Baraka, Skarlet, Erron, and Shao Kahn, D'Vorah arrives to rescue Shao Kahn's forces and Kollector, bringing them to her hive. Kotal and Raiden agree to work together and solve this crisis, with both Kitana and Jade staying in Outworld to aid Kotal, just as Raiden, Liu Kang, and Kung Lao return to Earthrrealm to learn more about their tragic future.
Back in D'Vorah's hive, Kollector tells Shao Kahn about how Kotal ascended to the throne and the whereabouts of Mileena. D'Vorah then tells Shao Kahn that after Kotal takes Shao Kahn's throne, she killed Mileena. But before Shao Kahn can attack D'Vorah for killing his daughter, Kronika appears before his forces, recruiting them for her cause.
Meeting with the Special Forces, Raiden learns the tragic events of the future he would endure, confirming what Kotal told him at Kotal's koliseum. Young Sonya learns that her future self was recently killed in action, and verbally tears into Cassie for abandoning her mother, causing Cassie to fire back that she only did so on her mother's orders. Liu Kang and Kung Lao are shocked to discover that their future selves have become undead revenants of the Netherrealm. Shortly after, the Special Forces are informed that the Netherrealm have invaded the Wu Shi Academy.
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