Two years after the defeat of Shao Kahn, Shinnok attacks Earthrealm with his army of Netherrealm demons, as well as the Earthrealm warriors who were killed during Kahn’s invasion and are now resurrected as revenants under Quan Chi’s control. After fighting their fallen comrades, a strike team led by Johnny Cage, Sonya Blade, and Kenshi open a portal to Raiden’s Sky Temple and head to the Jinsei Chamber, the source of Earthrealm’s life force, where Raiden and Fujin are seen battling Shinnok and his Netherrealm forces. When Shinnok tries to kill Sonya, Johnny rushes to defend her, inadvertently awakening ancient superhuman powers within himself. Using his newly-found powers, Johnny holds Shinnok at bay long enough for Raiden to steal Shinnok’s amulet and imprison him inside it, but Quan Chi escapes. Johnny, Raiden, and Sonya track him to his lair in the Netherrealm and defeat him, successfully restoring Scorpion, Sub-Zero, and Jax to human form in the process, though Quan Chi escapes again. In the years that follow, Johnny and Sonya marry and have a daughter, Cassie, though they later divorce. Scorpion reinstates his Shirai Ryu clan while mentoring Kenshi’s son Takeda, and Sub-Zero becomes the new Grandmaster of the Lin Kuei after killing Sektor.
Twenty years after Shinnok’s defeat, Johnny assembles a team of fighters composed of Cassie, Takeda, Jax’s daughter Jacqui, and Kung Lao’s cousin Kung Jin. After undergoing a training exercise with Sub-Zero, they are deployed to Outworld to resolve a civil war between former empress Mileena, who has obtained Shinnok’s amulet from Kano, and Outworld’s current emperor Kotal Kahn, with whom Earthrealm has a peace treaty. Meanwhile, in an Outworld refugee camp in Earthrealm, Sonya captures Kano and forces him to reveal Mileena’s location. Using this information, Cassie’s team aids Kotal in recovering Shinnok’s amulet and capturing Mileena, who is subsequently executed on Kotal’s orders. No longer believing Earthrealm capable of keeping the amulet safe, Kotal decides to keep it in Outworld’s hands, and takes Cassie and her friends hostage as leverage against Raiden. Kotal’s second-in-command D’Vorah, who is revealed as a double agent for Quan Chi, steals the amulet. Cassie and her team escape captivity, and inform Earthrealm of D’Vorah’s intentions.