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.
Back in the Special Forces base, past Jax tests his new cybernetic arms, and Jacqui talks with him about what happened to the present Jax: since his traumatic experiences as a revenant, and worst of all, the death of his wife Vera a year prior, Jax has become a shut-in, only feeling safe at the Briggs' farm.
Johnny starts to find common ground with his past self as they jointly admire Sonya, before the younger Cage ruins it by being crass and boastful. Johnny hauls him out to teach his younger self a lesson. Suddenly, the base is attacked by the Black Dragon and the Cyber Lin Kuei. The two Johnnys put differences aside, and fight back against the Black Dragon, before the younger Johnny is grazed on the cheek by a bullet, causing a faded scar to appear on the same spot for the present Cage. Driven into a rage, the younger Cage charges headlong into the melee, firing wildly and pushing back the Black Dragon henchmen, leaving his older counterpart to deal with the past Erron Black, who is still affiliated with the criminal group. Johnny questions the gunslinger's allegiance, since his present counterpart remains in a tenuous alliance with Earthrealm by virtue of staying in Kotal Kahn's service. Black responds that he always picks winners, to which Johnny counters that he chose poorly after defeating him. The elder Cage finds Cassie, alive but injured, who informs him that past Sonya has been captured. Johnny heads out to rescue her, commandeering a tank on his way to deal with the Cyber Lin Kuei.
Johnny's tank is taken out of commission when Sektor calls in a missile strike from an aircraft, but Johnny in turn lures the plane in and destroys it, evening the odds. Confronting the leader of the Cyber Lin Kuei, Johnny beats the cyborg, before he's challenged by the past Kano, who eats a punch to the groin for his troubles. Angered by the thug's threat to his wife and daughter, the Cage patriarch beats him down, before pressing a boot to his neck. Unfortunately, he is interrupted by a bullet to his knee, fired by the present Kano, who has also taken the younger Johnny hostage. The Special Forces have no choice but to watch as the Black Dragon leave with the past Sonya and Johnny in their clutches. Fortunately, Cassie places a tracker on their aircraft as it flies away.
However, their troubles are not over, as Kano had fitted Sektor with a nuclear bomb, which he activates during his exit. They are saved by the timely arrival of Raiden, who teleports them to the Shirai Ryu Fire Garden seconds before the explosion. The present Johnny Cage is out of commission for the rest of the battle to stop Kronika, recuperating from his injuries. As Raiden’s Sky Temple, Sub-Zero’s Lin Kuei army and Special Force HQ had been compromised, Hanzo welcomes the surviving Earthrealm allies to the Shirai Ryu's Fire Garden as the only safe haven left. The surviving Earthrealm’s heroes learns from the past Raiden that the other Elder Gods have ceased to exist, and Cetrion and Shinnok are Kronika’s children, realizing the fallen god's mother was directly responsible for one of the heroes’ past tragedies in many timelines. Raiden told his warriors that the traitor Cetrion informed him of Shao Kahn captured both Kotal Kahn and younger Jade. The younger Liu Kang ask Raiden to send him and younger Kung Lao back to Outworld and reunite with younger Kitana. Raiden is pleased and pray his Shaolin disciples to return victorious, almost slipped his mind to forget his fellow gods no longer exist anymore, but himself.
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