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.
Raiden, Fujin, Shang Tsung and the others were seen preparing to battle Netherrealm's demons. Fujin wears the crown to prepare to open the gates of Kronika's Keep. After doing so, present Jax tells Raiden and others that he will stay to keep in company with Fujin. When fighting, Raiden tells revenant Liu Kang that the cycle that Kronika placed him and Liu Kang to fight each other must end. As Liu Kang rushes towards Raiden, he fell down with a broken left leg. As seen in one of Kharon's ships, Shao Kahn smashed past Liu Kang's right leg, in which the revenant Liu Kang tells Raiden that Shao Kahn smashed both of his legs. Raiden, becoming furious, sees Shao Kahn and Sindel leaving Kharon's ships. Following this, Kotal was executed by decapitation. As Sindel and Shao led the charge against Earthrealm's forces, Raiden tells Fujin that he need to use the crown against Shao Kahn and Sindel. Fujin gives Raiden the crown, only to find out that it was Shang Tsung who was impersonating Raiden to get the crown off from Fujin. When Raiden discovered that Shang Tsung deceived them the whole time by freeing Shao Kahn, Shang Tsung then wears the crown at the right moment to superpower himself, claiming to be as equal as Kronika herself. Fujin realized that this was all been Shang Tsung's endgame, from the moment he was trapped in the Time Void. As Shang Tsung wields the Crown, he overpowered Raiden, Fujin and Jax.
Nightwolf faces Shang Tsung after he deceived the group in taking the crown. Nightwolf was then defeated and knocked out. As Shang Tsung was trying to steal Nightwolf's soul, Raiden and Fujin intervened. Shang Tsung defeated them and then drains their powers from them, which made them old and wrinkled. Instead that Shao Kahn and Sindel finishing them, Shang Tsung plans on draining their powers from them for eternity.
Later on, he, Shao Kahn and Sindel bursts into to the Hourglass. Cetrion allowed Kronika to absorb her essence in an attempt to strengthen her mother and the remaining revenants so they could defend the Hourglass. The revenants Kitana, Kung Lao and Jade tries to stop them, but all three of them died. Shang Tsung weakens Kronika, and only then betrays and defeats Shao Kahn and Sindel, telling them that killing Kronika is his destiny. After their defeat, he then tells them that his service to them is over, and that their service to him begins. Shang Tsung then takes their souls, leaving them as withered husks. He confronts Kronika and offers her to either serve him in his New Era or be wiped from history. When Kronika refuses to submit, Shang Tsung defeats her and steals her soul.
As Shang Tsung prepares to use the Hourglass, Fire God Liu Kang comes from his past to battle Shang Tsung. In confrontation, Shang Tsung realized Liu Kang allowed him to progress as he did for the latter to claim the crown, at the cost of losing his friends. The sorcerer complimented the Fire God's deviousness, as he was challenged by him in battle. Shang Tsung is erased from existence, and Liu Kang creates a new era where he meets his ancestor, the Great Kung Lao.
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