Johnny and his companions are ambushed by Scorpion and a revanent Sub-Zero, but he manages to fend them off. As they approach the temple, they are attacked again by revenants of Jax, Smoke, and Nightwolf. When Jax goes after Sonya, Johnny intervenes and drives him away.
Quan Chi and Shinnok reach the Sky Temple's Jinsei Chamber, and the fallen Elder God is poised to dispose of Raiden and Fujin until Johnny intervenes. When Shinnok tries to kill Sonya, Johnny jumps in the path of his magic attack, his body enveloped in a green aura that protects him. After fighting Shinnok to a standstill, Johnny takes Shinnok's amulet and gives it to Raiden, who seals Shinnok within it. With Shinnok's new imprisonment, the battle ends, but the war rages on: Quan Chi escaped in the chaos. While Sonya recovers in the Jinsei Chamber from her injuries, Johnny stays with her. Even though the fighting has not yet ended, he has a reason to smile:
"She called me 'Johnny'..."
Twenty-five years later, Johnny now commands a new generation of Special Forces: Cassandra Cage, his daughter with Sonya; Jacqueline Briggs, daughter of Jax; Kung Jin, a cousin of the late Kung Lao; and Takeda Takahashi, son of Kenshi and a disciple of Scorpion's Shirai Ryu. Trouble is brewing in Outworld, but the Lin Kuei have gone silent. Thus, Johnny tasks Cassie and her team with going to their temple to make sure the grandmaster, Sub-Zero, is still on their side.
The Special Forces are recalled at the behest of General Sonya Blade as Outworld refugees start coming to Earthrealm to escape the war between Kotal Kahn and Mileena. According to the refugee leader Li Mei, Mileena wielded a weapon, the description of which matches Shinnok's amulet. Although it shouldn't have been stolen with all the protection placed on it, Raiden leaves to verify if it has, indeed, been stolen. Li Mei also mentions an Earthrealmer among the refugees with an eye that glows red, who Sonya immediately recognizes as Kano. Meanwhile, Cassie's team is charged with going to Outworld.
Jin, as it turns out, has a very personal reason for freeing the bread thief: several years ago, he was a thief, himself. He broke into the Sky Temple one dark and stormy night to steal an heirloom of his cousin Kung Lao, but was confronted by Raiden, whom Jin blamed for Lao's death. The two came to blows, with Raiden allowing Jin to defeat him so he could dispel his anger and be more open to reason. Raiden encouraged Jin to put aside his life of crime and join the Shaolin. Although reluctant because of his past deeds and his sexuality, Jin took Raiden up on his offer.
In the present, Kotal Kahn, mistrusting of the Earthrealmers because of the earlier interruption of an execution and cross about Mileena's theft of the amulet they were supposed to protect, deems Cassie and her team to be allies of Mileena and sentences them to death. Jin, however, demands a trial by kombat to prove their innocence. In the ensuing duel, Jin emerges victorious. Kotal deems them innocent and leaves himself to Jin's mercy. Jin decides to spare Kotal's life and ask for his aid, instead, as Mileena posed a threat to both Outworld and Earthrealm so long as she had Shinnok's amulet.
Twenty years ago, Johnny and Sonya infiltrated Quan Chi's fortress. Therein, they are attacked by the sorcerer and three of his revanents: Scorpion, Sub-Zero, and Jax. While Sonya fends off the undead Shirai Ryu and Lin Kuei, Johnny is stabbed by Jax, and a revenant begins to form of him as his life ebbs away. After Sonya fends off Jax, Raiden appears to reverse the dark magic being placed on Johnny. Quan Chi intervenes, but Sonya defeats him, and Raiden not only succeeds in saving Johnny's life, but also undoing the necromantic magic on Scorpion, Sub-Zero, and Jax, returning them to life and restoring their free will. Raiden hopes to be able to do the same with the other revenants.
Back in the present, the hunt is on for Kano, who is hiding among the Outworld refugees. They find him, and he offers information in exchange for freedom, and when that doesn't work, threatens Cassie. Sonya nearly beats him to death, but Johnny stops her. The battered Kano finally gives up Mileena's location, which Sonya passes on to Cassie in Outworld.
Some time before, Mileena was the ruler of Outworld, but proved to be a poor leader: the realm suffered under her reign. D'Vorah discussed this matter with two other members of Mileena's cabinet, Kotal and Reptile, but they are found by Mileena and demanded their execution. D'Vorah kills Mileena's enforcer, Baraka, and Mileena is thrown into a dungeon, her rule usurped and given to the young Kotal Kahn.
In the present, D'Vorah and Cassie engage Rain and Tanya. Both rebels are defeated and, at Cassie's insistence, spared. Fate is not so kind to Mileena, whom D'Vorah captures and, by Kotal Kahn's demand, executes. Afterwards, Kotal has Cassie's team captured and imprisoned: he declares that he will be the new guardian of Shinnok's amulet, and will talk with Raiden about the team's fate.
Unbeknownst to the Kahn, D'Vorah is actually allied with Quan Chi and the Brotherhood of Shadow: she kills the guards watching over Shinnok's amulet and escapes with it.
Five years ago, Takeda was training with the Shirai Ryu, having been left in the care of the reformed Scorpion and clan leader Hanzo Hasashi by his father, Kenshi. After completing his training, he is approached by Kenshi, with whom Takeda is cross for seemingly abandoning him after his mother's death. Hanzo explains that his mother had been murdered by the Red Dragon clan, and Kenshi left him with the Shirai Ryu for his own protection. Kenshi promises his son that, one day, they will hunt down the Red Dragon together.
Back in the present, Takeda and his teammates are attacked by Erron, Reptile, and Ermac: they found the dead guard, discovered the amulet was missing, and pointed the blame towards the team. Takeda fends them off, but Kotal Kahn comes to believe D'Vorah is working for Raiden, and gathers his army for an invasion of Earthrealm.
Some time earlier, Hanzo had visited the Lin Kuei temple at the behest of Sub-Zero. He was reluctant and suspicious of the Lin Kuei grandmaster's offer to put the past behind them and forge a new alliance between the Lin Kuei and Shirai Ryu, and his misgivings seem confirmed when he is ambushed by the hot-headed cryomancer Frost. Sub-Zero subdues her, however, and reveals that after he killed Sektor and retook control of the Lin Kuei, he found a recording in the cyborg's computer brain that revealed Quan Chi's complicity in the Shirai Ryu's destruction and Hanzo's death. Shocked at this information, Hanzo pledges to see Quan Chi brought to justice.
In the present, Hanzo soundly beats Quan Chi. However, D'Vorah appears and tosses Shinnok's amulet to Quan Chi, the sorcerer completing a spell to release Shinnok in the moments before Hanzo beheads him. Free again in Earthrealm, Shinnok captures Johnny Cage and defeats Sonya before leaving for the Sky Temple. Cassie and her team arrive just as Shinnok disappears with Johnny in tow.
Back to the present, while recuperating in the Jinsei chamber, Bo'Rai Cho is attacked by Shinnok, who then proceeds to neutralize Raiden with the help of D'Vorah (who was carrying an incapacitated Johnny Cage) and the revenants Smoke, Kung Lao, Liu Kang, Kitana and Sindel. However, as Raiden is left alone and bullied by the revenants, he starts fighting, incapacitating Kitana, Smoke and Sindel and beating up Kung Lao and Liu Kang, but not before the two revenants call the thunder god out for leading them to their deaths. Shinnok then walks into the Jinsei and proceeds to corrupt the life force of Earthrealm, gaining immense power and transforming into a frightening monster in the process, while Raiden is captured by one of Shinnok's bone hands.
With this new power, Cassie is able to defeat the fallen Elder God. She and Jin then help Raiden reach the Jinsei, where he is able to cleanse Earthrealm's energy of Shinnok's corruption. The revenants retreat, Jacqui and Takeda nurse their wounds, and Sonya arrives to help Johnny and capture Shinnok and D'Vorah.
Although the crisis has been averted, purifying the Jinsei has changed Raiden. The thunder god, now bearing a more menacing appearance, confronts the new rulers of the Netherrealm, Liu Kang and Kitana, and warns them that he will no longer simply react to threats, but seek them out and destroy them outright. He presents the severed, still-living head of Shinnok as an example, warning them that there are fates worse than death.
