Each chapter focuses on one or two characters from the series and contains a combination of battles and extended cutscenes. Mortal Kombat 11 and the Aftermath expansion also have chapter titles in addition to the names of the aforementioned playable characters.
Some time after Cassie Cage defeated Shinnok and saved Earthrealm at the end of Mortal Kombat X, Dark Raiden is torturing the fallen Elder God with lightning at the top of the Sky Temple. In spite of his pain, Shinnok taunts that Raiden should thank him, as his corruption changed him for the better - now that the Thunder God wears his amulet, he has embraced the truth that the other Elder Gods cast him out for speaking. Raiden replies that the truth he has embraced is that anyone who endangers Earthrealm does not deserve mercy, and that starting with him, he will destroy any potential threats before they can destroy him.
Shinnok mocks Raiden, stating that Elder Gods cannot be killed, but Raiden responds that there are fates worse than death before beheading Shinnok with an energy blade. He declares to the fallen Elder God that he will deliver him to Liu Kang and Kitana in the Netherrealm as a warning of his wrath before departing. However, as he leaves, time freezes, and a mysterious woman arrives in the Sky Temple and hovers over to Shinnok's head. She takes pity on him, stating that he was not supposed to meet his fate and that Raiden has upset the balance of history, but assures Shinnok that the universe bends to her will, and that it is only a matter of time.
Two years later, inside the Special Forces Desert Command base, the Special Forces, with Johnny Cage, Cassie Cage, and Jacqui Briggs among them, take positions as Sonya Blade arrives to salute them. She explains that while in the past they have successfully protected Earthrealm from both Shao Kahn and Shinnok, none of these victories came without cost - in the case of the latter, Jax Briggs has been honorably discharged from the Special Forces, due to both physical and mental trauma from his time as a revenant rendering him unfit for duty. Sonya continues that they must honor his sacrifices by continuing their duty, and tells Cassie that while she has earned the promotion to Commander, she must first defeat the commanding officer in combat by Special Forces tradition. Cassie manages to defeat her mother and earn the rank of Commander, with Johnny congratulating her.
Later, Cassie and Sonya say their goodbyes to Johnny, who is leaving for Hollywood to star in the next Ninja Mime film, but are suddenly visited by Dark Raiden, who informs them that the Netherrealm is planning to invade. While Cassie suggests they attempt to negotiate with Liu Kang and Kitana, Raiden declares them irreparably corrupted by Shinnok's evil, and deems striking first the only answer - his plan is to assault the Cathedral of Shinnok, which is located underground beneath Liu Kang and Kitana's castle and is the source of their undead army's power, and destroy it to prevent them from being a threat. He offers to provide a distraction outside while the Special Forces sneak inside, as while he will be weakened outside of Earthrealm, he has Shinnok's amulet to make up for his weakness. While Cassie and Johnny are unsure, as they have become tired of Raiden's corrupted personality and are worried they will be discovered and trapped inside, Raiden counters that he understands what it means to lose someone.
Raiden transports himself, Sonya, Cassie, Jacqui, and several Special Forces platoons into the Netherrealm, where he assaults the Netherrealm's army outside the castle as the others sneak inside and descend into the Cathedral. However, they find it guarded by Kabal, Jade, and a large group of undead. Sonya tells Cassie and Jacqui to distract them while she and a platoon sneak past and plant C4 on the support, and they open fire. As Jacqui engages Jade, Cassie fights and defeats Kabal, with the rest of the Special Forces defeating the army. However, Sonya finds the support columns are too far apart and needs extra time, while Jade manages to escape and warns Liu Kang and Kitana of the surprise attack. The Special Forces manage to set an ambush with extra C4 for the next wave of undead, and Cassie manages to defeat Kitana.
However, Liu Kang ambushes Sonya's platoon as they are heading out and uses a torrent of fire to collapse the ceiling, burying everyone alive, before turning to confront Cassie. She manages to defeat the fallen Shaolin monk and attempts to dig out the rubble, but Sonya contacts her from inside - the rest of her platoon is dead, and she knows she won't survive. Despite Cassie's best efforts, Sonya begs Cassie to save herself and the other Special Forces as her final wish before cutting the channel and activating the C4. Jacqui manages to bring a grieving Cassie to her senses, and the survivors of the assault retreat outside to Raiden to be transported back. Johnny arrives to greet them, only to find out what happened. The Cage family mourn Sonya's death, only for Raiden to state that she was lucky to die a warrior's death, causing everyone to lose his respect.
Back in the Netherrealm, Liu Kang and Kitana stand amidst the ruins of their castle, vulnerable without its power, when they are suddenly surrounded by a blizzard of sand, the mysterious woman from the prologue forming from it. She reverses time to restore the Cathedral to its former glory, and introduces herself as Kronika, the Keeper of Time. Transporting the two to her Hourglass, she explains that her role is to guide the Sands of Destiny inside to ensure the destiny of every soul and realm remains in balance, but Raiden has irreversibly tainted them through his actions in the previous two games. Kronika plans to erase the timeline and start again from the beginning, and convinces Liu Kang and Kitana to promise the Netherrealm's allegiance after assuring Raiden will not exist in her "New Era", thus preventing their unjust deaths.
Meanwhile in Outworld, Kotal Kahn has captured and sentenced the Kollector, one of Shao Kahn's loyalists, to death in the Kahn's Arena. While Kollector argues that he obeys Shao Kahn's word, Kotal reponds that Shao Kahn is already dead, and that Shao's corrupt law allowed Kollector to get away with stealing from those weaker than him. As Kollector struggles to free himself from the apparatus meant to snap his neck, Kotal sees that his soldiers are struggling to turn it and prepares to behead him with his Macuahuitl when suddenly the ground starts to rumble, and a blizzard of sand surrounds the Arena. At the same time, Cassie, Johnny, and Dark Raiden awaken to see a similar sandstorm throughout the Special Forces base. These actions are caused by Kronika using the Hourglass to merge the Sands of Destiny, merging the past and present together.
The sandstorm rages on, but to the everyone's shock, the sand appears to take form, creating younger versions of Johnny, Sonya, and Jax, who can only stare in confusion and bewilderment - shortly afterwards, Dark Raiden can only gasp in shock as his own body disintegrates into the sands, leaving behind Shinnok's amulet once the sandstorm dissipates. Back in Outworld, Kollector uses the distraction of the sandstorm to break free from his apparatus, and the sand takes several forms - before everyone, younger versions of Skarlet, Erron Black, and Kano appear, alongside Shao Kahn and Baraka, alive once more. However, the sand also creates younger versions of Liu Kang, Kitana, Kung Lao, and Jade, alive unlike their present counterparts, alongside a younger Raiden who has yet to become corrupted.
Kotal is bewildered to see a barrage of past faces, but Shao Kahn takes immediate offence - not only has Kotal taken his throne, but both he and Mileena will die. Raiden explains that they were at the second Mortal Kombat tournament, where Kung Lao had just defeated both Shang Tsung and Quan Chi in kombat. Kotal is also overcome with joy to see Jade, his long-gone lover, brought back alive, but the moment is interrupted by a furious Shao Kahn, who believes Raiden has trapped everyone in an illusion and demands Kotal relinquish his throne. A fight then breaks out between Shao and Kotal - the latter is losing the fight, but Raiden and Liu Kang save him, and a fight breaks out between the two sides. In the chaos, Kotal confronts Baraka, who is distraught to learn he and his other Tarkata die, and defeats him.
However, Kotal is suddenly caught by a rush of blood that erupts from a dead beast, and is washed down into the beast pens below the Arena where he confronts Skarlet and defeats her. Jade manages to meet with him, where Kotal explains that he was captured and taken to Shang Tsung's Flesh Pits for experimentation, but was freed following the sorcerer's death. As she returns to the surface to help the others, Kotal confronts Erron Black - while he tries to reason with the cowboy, telling him that he becomes a future ally, Erron responds that he doesn't care about the future and only wants to be on the winning side. Kotal defeats Erron as well, and returns to the outside to confront Shao Kahn. While Shao Kahn is outraged, believing Kotal is unworthy of Outworld's throne, Kotal responds that Shao Kahn was a corrupt and unjust dictator who only cared about himself, not the people he ruled over.
Shao Kahn is defeated, but before Kotal can finish him, D'Vorah comes to the aid of the villains and leads them through a portal of sand, taking them to safety. With the conflict over, Raiden introduces himself, but Kotal rebukes that he already knows who Raiden is and explains to the Thunder God how he becomes corrupted and apathetic following Shinnok's defeat, which horrifies him. Regardless, Raiden assures Kotal that he is not the person he is yet to be, and the two form an alliance to find out what has happened - Raiden prepares to return to Earthrealm with Liu Kang and Kung Lao to find out what else has happened, with the former bidding goodbye to Kitana as they wish each other luck.
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