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.
Liu Kang tries to reason with Raiden, saying that Scorpion may be telling the truth. Raiden doesn't listen and attacks Scorpion using Shinnok's amulet. After Liu Kang tries to stop him, Raiden attacks him with the amulet as well, saying that their time has run out and he has got to save Earthrealm. After the battle, Liu Kang decides that the Revenants were actually right, and that Raiden cannot be trusted. Raiden replies that he does not need trust, but demands obedience, his eyes and lightning now glowing red. As Liu Kang prepares to use his fire power against him, Raiden comes to a realization: "This has happened before". He begins seeing visions of both himself and Liu Kang fighting each other in various places and alternate timelines. The most notable locations are the Rooftop from Mortal Kombat (2011), the Pyramid of Argus from Mortal Kombat: Armageddon, and supposedly, Apokolips from Mortal Kombat vs. DC Universe. Recoiling in horror, Raiden drops Shinnok's amulet.
He realizes that the only reason why he and Liu Kang were fighting was because Kronika wants it. After that, he proceeds to heal Scorpion and apologizes to him, saying that he was also a slave to anger. While Liu Kang and the others initially fail to understand what is happening, Raiden explains that Kronika has restarted time on multiple occasions, with each timeline pitting him and Liu Kang against each other, and Liu Kang dying in each battle. Just when Raiden assures the others that Kronika will no longer control them, time is frozen and everyone else along with it, with the exception of Raiden. Kronika arrives, and tells the Thunder God that the combined powers of both Raiden and Liu Kang pose a threat to her vision of the timeline, which is why she has always set them against each other. Raiden then threatens her that this timeline will end differently, but Kronika rejects his claims, stating that they have had the same conversation multiple times, but it has never changed the outcome. She then challenges him to confront her one final time, but without Liu Kang by his side. As time resumes, Kronika takes Liu Kang to her isle, where his revenant counterpart steals his soul to increase his own strength.
Shortly after, Raiden and his allies are on board Kharon's fleet for the final battle. But against them, Frost and Geras are leading a large ship with Cyber Lin Kuei warriors. Kharon says that his fleet is not prepared for battle, but Raiden assures him that the ships will be protected by the combined forces. As the ships collide, the Cyber Lin Kuei attack. Present day Jax is then sent to fight Raiden in a losing effort. Raiden successfully convinces him that Kronika has manipulated him all along, which causes Jax to turn on Kronika's forces. Then Geras fights and loses to the Thunder God, who binds him to a chain and anchor. While Geras says that drowning cannot kill him, Raiden replies that the Sea of Blood is bottomless and he will sink forever. After this, he is dragged into the Sea of Blood. Frost then appears to Raiden, telling him that the Cyber Lin Kuei are under her command and challenges him. After her defeat, Raiden short circuits Frost's mind, which causes the connection to sever, and the Cyber Lin Kuei army to shut down.
In the meantime, the revenant Liu Kang has absorbed the soul of his mortal counterpart and goes after Kharon's fleet to challenge Raiden. When the two confront each other, Liu Kang attacks Raiden knocking him back. Raiden is shocked that Liu Kang has taken his own soul, to which Liu Kang replies that this was a lesson Raiden taught him: to fight his enemies by any means necessary. After defeating the revenant, Raiden tells Liu Kang that he has overcome the darkness within himself and that Liu Kang must do the same. While Liu Kang demands him that he has to kill him, Raiden says that he'd rather save him and not repeat the same event all over again. He grabs and encircles Liu Kang in a lightning force field. During this, the mortal Liu Kang gets teleported out of Kronika's Keep to the lightning force field. Shortly after, the force field dissipates. The result is a merged form between Raiden and Liu Kang – Fire God Liu Kang.
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