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.
In the Outworld castle, Sindel secretly spoke with Shang Tsung on how Kitana was a fool for working alongside with Raiden. After her conversation ended, Kitana entered her room and Sindel falsely greeted her. When Shao Kahn was being tortured by two Shokans, Sindel killed them to rescue Shao Kahn. The two planned on dethroning Kitana. As Sheeva overheard the conversation, the two clashed, leading to Sheeva's defeat. More Shokans arrived and discovered Sheeva's unconscious body. Sindel pins the blame on Kitana, leading the Shokans to join her against Kitana to avenge Sheeva.
Geras, wearing new armor, confronts Sindel and the rejuvenated Shao Kahn in the Soul Chamber, and demands their services to Kronika. Feeling betrayed by Kronika due to Kitana gaining the Outworld throne, Shao Kahn refuses his services and instead decides to attack the construct with Sindel. Being defeated, Sindel knocks a weakened Geras away where Shao Kahn approaches and mercilessly beats a downed Geras over the head repeatedly with his Wrath Hammer, completely destroying his head with one final slam.
Shao Kahn and Sindel went on a mission to intervene in the battle between Raiden and Kronika's forces to seize the Hourglass for themselves. They defeated Sonya, Cassie, and past Johnny, seizing their ships that they were planning to take across the Sea of Blood. Dumping cargo to increase their speed, they caught up to Kitana Kahn's ship. While Kitana lost contact with the Shokan, Commander Cage, and the Special Forces, Kung Lao suspected Sindel's betrayal, but Kitana denies it. Kitana uses her scope to check the incoming fleet, only to discover Sindel's betrayal. In the keep, Kronika manipulate all Outworlders to fight against each other with the Hourglass.
Boarding the vessel, Shao Kahn brutally struck down Kotal, and Sindel defeated Jade. They fight Kung Lao, throwing him overboard after his defeat. Kitana pleaded her mother to stop the chaos and questioned what spell had Shao Kahn used on her. In reality, Sindel was never bewitched. She willingly married Shao Kahn. She explained why she betrayed Jerrod and to strengthen her bond with Shao Kahn, she helped him murdered her former husband. Much to Kitana's disgust, she clashed with her mother and was defeated. Shao Kahn clashed with Liu Kang and defeated him. He and Sindel then convinced all of Kitana's soldiers (Osh-Tekks and Tarkatans) that Kitana was the traitor and a bad leader. Sindel wanted Kitana to be put in chains to suffer the 'anguish of defeat'. With all of her soldiers betraying her, Kitana reached for Liu Kang's hand, only for Shao Kahn to crush it.
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