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.
On their way to the Wu Shi Academy, the past Liu Kang and Kung Lao begin lamenting their dark futures. Liu Kang decides to continue to put his faith in Raiden, but Kung Lao begins feeling skeptical.
Upon infiltrating the academy, the Shaolin Monks encounter the same Scorpion from their timeline. One of the monks works to disable the traps while the other fights Scorpion, at first to no avail, until the arrival of revenant Jade, who is under Kronika's orders to keep the Shaolin Monks alive. This allows the two an opportunity to make the revenant Edenian and the time-displaced wraith retreat.
The duo then come across Geras, who is stealing vials that contains Earthrealm's life force, the Jinsei. Geras knew they were coming, however, due to the revenant versions of Liu Kang and Kung Lao. After defeating their counterparts, the two then fight and defeat Geras before he freezes them in time.
Kronika appears and although Geras states that it would be dangerous to let them live, Kronika keeps them alive, as if they die, their revenant counterparts would cease to exist. Geras and Kronika disappear as time resumes for the duo.
Back at the Special Forces Desert Base, Liu Kang, Kung Lao, Sonya, Cassie and Johnny Cage learns that the realms are in crisis. Raiden will find a way how to solve it.
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