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.
Sub-Zero is in a quarry, monitoring the recently reactivated Cyber Lin Kuei factory. Hanzo Hasashi, Scorpion's living present-self then arrives, and enquires as to the whereabouts of Sektor, as he doesn't want him to threaten his clan again. Sub-Zero informs Hanzo that, while the factory had been previously shut down and buried in the quarry, when the time merger restored Sektor, he reactivated the facility, and kidnapped Lin Kuei warriors to be turned into cyber slaves. He tells Hanzo of his plan to infiltrate the factory – an assault on the main entrance will be bloody, so he proposes to enter via a less-populated entrance, and obtain help from the inside.
Both enter the factory, only to find dismembered bodies lying on the ground. Hanzo swears to Liang that they will avenge the dead Lin Kuei. Both hide as Cyrax and an unknown cloaked figure arrive to create more cyber warriors. Sub-Zero tells Hanzo that if they disable Cyrax's behavior inhibitors, he'll have his humanity restored and turn on Sektor, and will be able to shut the Cyber Lin Kuei down, as all cyber warriors are linked to a common network. They split up, with Hanzo focusing on Cyrax, while Sub-Zero is dealing with the cloaked figure, who is revealed to be Frost. He accuses her of betrayal after all he did for her, whilst Frost counters by accusing him of corrupting the Lin Kuei in making peace with Hanzo, and that with Kronika's help she will restore the clan's "honor". Sub-Zero informs his former student that there is no future in which she could be the head of the clan, with Frost replying that he has always doubted her and that Kronika saw her real potential from the start. After defeating Frost, Cyrax reappears with some activated Cyber Lin Kuei warriors, saying that they are defending Kronika's cause, and that the new Cyber Lin Kuei will help usher in the New Era. The chosen character will fight Cyrax while the other will deal with the remaining cybernetic warriors. Sub-Zero berates Cyrax for being enslaved by Sektor and Kronika, and vows to end this. After Cyrax's defeat, Sub-Zero begins to disable the behavior inhibitors. Hanzo is attacked by a newly-arrived Noob Saibot, who claims that in the New Era, Kronika will make sure that he would lead the realm's deadliest clan of wandering shadows, before he is defeated by Sub-Zero/Hanzo. Noob taunts Hanzo, claiming that without Quan Chi's influence Hanzo is weaker. After Noob is defeated, Cyrax comes to, and realizes with horror what has become of him. He learns what he needs to do to destroy the Cyber Lin Kuei, before Sektor fires rockets at the trio, which Cyrax stops by using his net. Sektor had been warned by Frost that Sub-Zero and Hanzo had become allies, and was astonished at Sub-Zero engaging in an "act of dishonor". : Sektor was revealed to be the one who started the massacre on the first Shirai Ryu by setting it on fire, vowing that he will finish what Quan Chi failed to accomplish in their deal. After Sektor is defeated, Cyrax manages to get into the Cyber Lin Kuei servers, and informs Sub-Zero that he can disable the factory, but he states that if he is brought back, he doesn't want to live as a cyborg. Sub-Zero reassures Cyrax that, whether he is machine or man, he has a warrior's spirit, and will be welcomed into the Lin Kuei as long as Sub-Zero is grandmaster.
Cyrax then destroys the main power source of the factory, which disables Cyrax and the rest of the Cyber Lin Kuei, including Sektor, who is transported back to Kronika's lair by Frost and Noob. Sub-Zero and Hanzo discuss what they should do next, both agreeing that they should inform Raiden of their accomplishment.
Back at Kronika's lair, Geras questions a younger Kano and Erron Black about if they can restore Sektor, and whether he can be copied thousands of times. Suddenly, the older Kano appears, and tells them that they should agree to serve Kronika.
In the Briggs house, present-day Jax tried to contact her daughter, Jacqui, but her phone was lost connection due to the time quake, which made him frustrated about it. Moments later, Kronika recruits the present-day Jax to her side.
Raiden had a conversation with Kotal, Jade and Kitana in Outworld, about stopping Shao Kahn from reclaims the throne.
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