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.
Shang Tsung, Fujin, Nightwolf, and Sindel has arrived to his island, now in ruins, to find Kronika's Crown. They are ambushed by the revenants Kabal and Jade, but manage to defeat them. Nightwolf and Sindel remains on the topside to deal with Cetrion, while Shang Tsung and Fujin search for the crown in Goro's Lair. While walking along the cavernous corridors of the lair, Fujin questions the sorcerer on how long he will betray them. They approach the Well of Souls, only to be confronted by Jax and Noob Saibot. Fujin defeats Noob and stops Shang Tsung from draining Jax's soul. After defeating Jax, Fujin managed to talk him into joining forces against Kronika. Outside, Sindel and Nightwolf are fighting Cetrion. After Cetrion subdues Nightwolf, he tries to sacrifice himself to defeat Cetrion, but Sindel intervenes and fights the Elder God. With Cetrion incapacitated, Shang Tsung, Fujin and Jax emerge from Goro's Lair and Shang Tsung teleports Cetrion away. With the Crown in hands, a Special Forces team led by Jacqui and past Jax ambushes the group, but present Jax manages to talk them down and explain the situation. Sindel has Shang Tsung send her back to Outworld and Nightwolf decides to accompany the Briggs', while Fujin and Shang Tsung go to the Fire Gardens to deliver the Crown to Raiden. At Kronika's Hourglass, Cetrion informs her mother of her failure in retrieving the Crown, with Kronika deciding that Shang Tsung is now too dangerous and that now she must take action.
In the Fire Gardens, past Scorpion surprises both Sub-Zero and past Liu Kang, who leaves to warn Raiden. Sub-Zero is distrustful of Scorpion, but before a kombat ensues, Shang Tsung and Fujin emerge from a portal, requesting to talk to Raiden. Believing this to be Shang Tsung's trick, Sub-Zero freezes the sorcerer and asks for Scorpion's assistance in fighting Fujin, but both are defeated. After their defeat Fujin frees Shang Tsung from being frozen with the help of his Plasma Crossbow. Raiden arrives with Liu Kang and questions Fujin on his allegiance with Shang Tsung. They present the Crown and voice their plan of using it to defeat Kronika, but Raiden, under Shinnok's amulet's influence, refuses to believe the sorcerer and attacks him. He tries to attack Liu Kang as well, but Fujin intervenes and defeats him. Regretful, Raiden puts down the amulet and realizes that he have let himself to become a slave to anger, within Shinnok's amulet. So he decides he won't use it anymore and to listen.
The warriors regroup and Fujin explains how Raiden turns Liu Kang into a Fire God, but before he could explain more, Kronika teleports to the Fire Gardens and freezes the warriors in time, sparing only Raiden, Fujin and Shang Tsung. Kronika confronts Fujin and Shang Tsung about her defeat and reveals that the Crown was Shang Tsung's design, before warning that he will eventually betray them. Raiden states that she will be finished and if Shang Tsung betrayed them, they will have to finish him too. They attack Kronika, but she freezes Raiden and Shang Tsung in time. She then create a sandstorm, which will end their existence. However, Fujin puts the Crown on before he is frozen as well and unfreezes Raiden and Shang Tsung, who both helped him in sending Kronika away. The other warriors are unfrozen and prepare for the upcoming battle at Kronika's Isle.
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