The story mode of Mortal Kombat (2011) contains 16 chapters total, telling a cohesive story recounting the events of the first three Mortal Kombat games, with both major and minor changes. Each chapter focuses on a single character from the series (except Chapter 11, with Liu Kang taking the final fight), and contains a combination of fights and extended cutscenes.
Below is a list that shows the chapters in order:
- Johnny Cage
- Sonya Blade
- Cyrax (Human)
- Liu Kang
- Sub-Zero (Kuai Liang)
- Kung Lao
- Cyber Sub-Zero
The story begins with the aftermath of the Battle of Armageddon, where nearly all of the kombatants have been killed. Only two kombatants are shown to have survived: the Thunder God, Raiden, and the Emperor of Outworld, Shao Kahn. Kahn had his powers increased by killing Blaze, and is currently engaged in a fight with Raiden, where he easily gains the upper hand and taunts the Thunder God, destroying his medallion in the process. Realizing the battle is lost, Raiden gathers up the shattered pieces of his medallion and sends a cryptic message to his past self, including the words "He must win", moments before Shao Kahn delivers a killing blow on him.
Chapter 1 - Johnny Cage
Raiden's message, alongside a series of mental images, travels back in time to the events of the first Mortal Kombat tournament covered in the series, held on Shang Tsung's Island. The Raiden of the past not only senses these visions but also notices that his amulet is cracked. He thinks nothing of it at first, as the tournament is beginning.
Shang Tsung appears with his monks to greet the kombatants and welcome them to the Mortal Kombat tournament. He also introduces himself as the final challenge of said tournament. Johnny Cage, after insulting Shang Tsung behind his back, is called forward to fight Reptile. Cage wins, and Shang calls in Baraka as his next opponent. Cage defeats Baraka and is ordered to 'finish' him, but does not comply. Immediately afterward, Cage is congratulated on his victories by Raiden, who along with Liu Kang, warns him that Earthrealm is in grave danger. He does not take their warnings seriously, however, and instead chooses to try to ask Sonya Blade out on a date.
The scene then cuts to a bridge over the Pit, where Cage is seen attempting to woo Sonya, much to her annoyance. She eventually becomes pissed off, leading to a fight between them. Cage wins the fight, but Kano appears behind him and throws him off the bridge, moving over to finish off a weakened Sonya. However, Johnny manages to fling himself back onto the bridge and defeat Kano. Sonya thanks him and reveals who Kano is.
Chapter 2 - Sonya Blade
Sonya then reveals she is looking for her superior, Jax Briggs, who is being held prisoner somewhere in the island. She departs with Johnny to look for Jax and finds him locked in a prison cell in Goro's Lair. As she tries to free Jax, Shang Tsung shows up and tells Sonya that he has been expecting her. She tries to tell him that she is not part of his plans and demands that he free Jax, to which Shang responds that Sonya is indeed a kontestant and that she will face Sub-Zero.
After Sonya defeats the Lin Kuei assassin, Raiden appears and receives yet another vision, this time of Liu Kang defeating Shang Tsung. Believing this means something, Raiden tries to prevent Sonya from attacking Shang, only to have the Special Forces lieutenant attack him instead. After ordering Sonya to stop, Raiden assists her in freeing Jax by creating a blinding flash of light. As Sonya and Jax flee, they are confronted by Kitana and Jade, but Sonya manages to defeat them both. A helicopter arrives shortly afterwards, only to be blasted out of the air by a fireball.
Sonya turns to Shang Tsung, who reveals to her that Kano is challenging her to kombat. Kano mocks Sonya for not having Johnny around to protect her. Sonya, however, defeats Kano and tries to take him into custody, but Shang intervenes. Kano then leaves with the sorcerer. Raiden, Liu Kang, and Johnny Cage show up, with the thunder god using his magic to heal an injured Jax. Raiden tells the group that he has been receiving visions from the future, about Armageddon, and believes they must work to avert this tragedy, starting by winning the tournament. Sonya, Johnny, and Jax all agree to work with Raiden.
Chapter 3 - Scorpion
The next day, the revenant Scorpion is summoned from the Netherrealm to fight in the tournament. He expresses a desire to battle Sub-Zero. Raiden, knowing that Kung Lao is in disguise as a Masked Guard standing beside him, confronts him. Lao, eager to prove that he is Liu Kang's equal, accepts the challenge against Scorpion, but loses. After humbling Lao in kombat, Scorpion once again demands a fight against Sub-Zero, only to be challenged by Nightwolf instead. The shaman tells Scorpion that his aggression is misplaced and that he should look for other ways to find peace instead of seeking revenge. Scorpion, however, simply accuses Nightwolf of dishonoring his own kind and defeats him. After the fight, Raiden, having sensed a vision that, if Scorpion kills Sub-Zero, a more dangerous threat will emerge, speaks to Scorpion and pleads with him to spare Sub-Zero's life, on the condition that he will ask the Elder Gods to resurrect the Shirai Ryu if he does. Scorpion reluctantly accepts this agreement.
The next day, Scorpion approaches Lin Kuei assassins Cyrax and Sektor, who promptly taunt him and his clan, leading to Shang Tsung declaring a kombat challenge. Scorpion soundly defeats both in a 2-on-1 fight. Not long after, Sub-Zero shows up and taunts Scorpion, who responds by dragging him to the Netherrealm where they engage in kombat. Sub-Zero is defeated, but Scorpion honors his agreement with Raiden and spares his life. Quan Chi, however, shows him images of the Lin Kuei's destruction of the Shirai Ryu, including one of Sub-Zero murdering his wife and child. Sub-Zero pleads with Scorpion for mercy and tells him the visions are fake, but Scorpion removes his mask in a fit of rage and proceeds to kill Sub-Zero.
Chapter 4 - Cyrax
A distraught Scorpion later returns with Sub-Zero's charred skull and spine and leaves soon afterward. Raiden then speaks to Sub-Zero's former friend, Cyrax, who vows to make Scorpion pay. In the discussion, Raiden asks Cyrax about the Cyber Initiative, and also questions the participation of the Lin Kuei in the tournament. Unfortunately, this conversation leads Cyrax to be ambushed later on by Sheeva and Baraka, who have been sent to kill him by Shang Tsung. However, Cyrax emerges victorious over both warriors.
Cyrax confronts Shang Tsung as he is conversing with Sektor. Tsung scolds Cyrax for having jeopardized his plans by speaking with Raiden. Sektor nevertheless explains that Cyrax will continue his mission, which is to kill Johnny Cage. Immediately afterwards, Cyrax fights and defeats Cage, but decides to spare Cage's life, leading him to rebel against his clan. Sektor confronts him over his disobedience, stating that the Cyber Inititiave will remove all insubordinance. Angered, Cyrax fights Sektor, defeats him in the process, and declares that he is done with the Lin Kuei.
Chapter 5 - Liu Kang
Liu Kang emerges as the only Earthrealm warrior left in the tournament. Shang Tsung introduces Ermac as Kahn's latest creation and has him fight Liu Kang, only to defeated by him. Watching the fight, Kitana tells Tsung she will ensure Liu Kang doesn't reach the final challenge. While training for the next fight in the courtyard, Liu Kang and Raiden discuss the Thunder God's visions more, especially the sentence of "He must win". Believing that "He" refers to Kang, Raiden further encourages him. Later, Kang is ambushed by Kitana, but manages to defeat her. When Kitana asks him to kill her, Kang spares her life. Instead, he remarks that they truly had no encounter, and expresses a desire to meet her under more favorable circumstances.
Kang later fights against his next opponents: Scorpion and Quan Chi, defeating them both. He is then sent to Goro's Lair to challenge the reigning champion, Goro. After a long, hard-fought battle, Kang defeats the Shokan prince. With this victory, Kang faces off against his last opponent: Shang Tsung himself. As Raiden foresaw, Kang bests the sorcerer, who concedes defeat, handing victory to Earthrealm. The Outworld warriors, along with Kano, leave through a portal, with Kitana taking a last lingering look before departing. Raiden and the other Earthrealm forces congratulate Kang on his victory, but to Raiden's surprise, his amulet cracks further.
Back in Outworld, Shang Tsung is brought before the emperor. Shao Kahn is angered and orders Kitana to execute him. In order to save himself from being executed, the sorcerer quickly makes a new proposition to Shao Kahn.
Liu Kang is presented at the ceremony as the new champion of the Mortal Kombat tournament, with Kung Lao, Johnny Cage, Sonya Blade, and Jax in attendance. At the celebration, Jax is having a victory cigar while Raiden is confused as to why his amulet is still cracked. Raiden then takes notice of a revitalized Shang Tsung, where the sorcerer proposes an offer from the emperor: He proposes a single tournament, replacing the original system of ten, and tells Raiden if Earthrealm wins the tournament, Kahn will forever have to abandon his claim to Earthrealm. However, should Outworld win, Kahn will be allowed to merge Earthrealm with Outworld.
Chapter 6 - Jax
Raiden dismisses the offer, which results in the Wu Shi Academy being overrun by Tarkatan warriors. In the chaos, Sonya and the Shaolin Masters are kidnapped and brought to Outworld. Raiden receives another image, showing Liu Kang winning the new tournament. He decides to accept the challenge, but concludes that he must change the outcome of this tournament, as Kang's victory over Tsung had no effect.
Raiden tells Liu Kang and Kung Lao to tend to their masters whilst he, Jax, and Johnny Cage go to Outworld to attend the tournament. Jax steps forward to find Sonya, only for Shang Tsung to declare this as Jax volunteering for first kombat. The first round of the new tournament sees Jax defeat Baraka, but the tournament is briefly put off after Reptile informs Shang Tsung of some "pressing matters".
Raiden teleports himself and the other Earthrealm warriors to the Armory after one of Raiden's visions reveals that Sonya was to be executed. Johnny Cage questions Jax about his relationship with her, to which Jax states that he is her commanding officer, nothing else. Jax becomes increasingly annoyed by Cage's gloating and they get into a fight, which is put to an end by Raiden. Jade appears and demands that the three leave the armory. However, Jax fights Jade and defeats her. After rendering Jade unconscious, Cage and Jax patch things up and the three continue their quest to find Sonya.
They eventually find Sonya tied to a stake by the Dead Pool, guarded by Sheeva and her minions. After killing one of the attacking guards and jumping over the rest of them, Jax fights and defeats Sheeva while Johnny and Raiden deal with the remaining guards. He then frees Sonya. Her wrist communicator picks up two tech readings from Outworld's shores. Since Outworld doesn't possess great technology, Raiden concludes that they might be helpful to look into, and goes with Johnny Cage to investigate one of the signals while Sonya and Jax take the other.
Chapter 7 - Smoke
These two readings lead them to the Lin Kuei warriors Smoke and Tundra, the younger brother of Sub-Zero who decides to take up the mantle of his older brother. It is known that they escaped from the Lin Kuei headquarters and are searching for information about Sub-Zero's death. The two split up, and Smoke is accosted by Kitana, who orders him to leave Outworld. Smoke responds by mocking her, then defeats her in kombat.
He then makes his way to the Living Forest, where Kano is selling advanced weaponry to Shang Tsung. Smoke confronts Tsung and demands the whereabouts of the original Sub-Zero. Kano volunteers to take care of the Lin Kuei for free, but is quickly defeated. Smoke then confronts Shang Tsung again. In response, Tsung morphs into Sub-Zero, with Reptile joining his side. Smoke subdues them both, only to be ambushed by Sektor, who is now a cyborg. He attempts to bring Smoke back to the Lin Kuei temple to undergo the same procedure. Smoke manages to defeat Sektor, declaring that he will never submit to the Cyber Initiative. However, a swarm of Lin Kuei cyborgs show up to take him back by force. Raiden, who received a vision of Smoke being turned into a cyborg, intervenes and takes the cyborgs out with a blast of lightning. A grateful Smoke agrees to join him and Johnny Cage in their quest, expressing fears that the younger Sub-Zero may be in danger as well.
Chapter 8 - Sub-Zero
The scene cuts to the Soul Chamber, where Sub-Zero is seen practicing his freezing powers. Suddenly, he is ambushed by a cybernetic Cyrax, but manages to defeat him just as Jax and Sonya arrive. Initially believing him to be the original Sub-Zero, they eventually explain his death at the hands of Scorpion. The three then encounter Ermac and, in the resulting confrontation, Jax has both his arms telekinetically ripped off his body. Sub-Zero then engages Ermac in kombat while Sonya tends to Jax. After winning, Sub-Zero tells Sonya and Jax a way out to Earthrealm while he goes to Shao Kahn's Coliseum in the hopes of exacting revenge against Scorpion.
Sub-Zero eventually reaches the Coliseum and wants to face Scorpion, but has Reptile fight him instead. Emerging the victor, Sub-Zero once again demands Scorpion as his next opponent, to which Shao Kahn agrees. Quan Chi summons Scorpion from the Netherrealm and the battle begins. Sub-Zero wins the match, but before he can finish Scorpion off, he is ambushed by cybernetic Lin Kuei warriors, who offered their allegiance to Shao Kahn in exchange for Sub-Zero. Sub-Zero disappears, along with the cyborgs.
Chapter 9 - Kitana
Since Kitana has been ordered to eliminate any Earthrealm intruders, she is scolded by Shao Kahn for failing to do her duty. As she leaves, the Earthrealm warriors follow her. After arguing with Jade, Kitana is confronted by Raiden and his allies. Determined to redeem herself to her father, Kitana fights and defeats both Smoke and Johnny Cage. Before she can finish them off, Raiden stops Kitana and has a talk with her to help her understand her true nature, discussing her deceased mother, Sindel.
To this end, he encourages her to go to Shang Tsung's Flesh Pits, a place she is forbidden to enter. As Kitana makes her way through the Living Forest towards the Flesh Pits, Jade reveals herself and pleads to Kitana to turn back by order of the Emperor. Kitana refuses and fights her, knocking her unconscious and then moving on.
When Kitana finally arrives at the Flesh Pits, she discovers a series of clones designed in her image but also sporting Tarkatan features. One of these clones, who looks exactly like Kitana, except for her eyes and mouth, wakes up. Believing it to be a monster, Kitana attacks it. Shang Tsung then confronts Kitana and tells her that he made the clones in an attempt to "perfect" her. Angered, she fights Shang Tsung, defeats him, and drags him to face judgement of Shao Kahn.
However, the emperor not only praises Tsung, but reveals to Kitana that he is not her biological father. Instead, she is the daughter of an Edenian king whose realm was conquered by Shao Kahn long ago, adopting Kitana as his own personal assassin after killing her real father. He then orders his minions to subdue Kitana and take her for execution, while demanding that his new daughter, whom he names "Mileena", be brought to him. Jade, overhearing Shao Kahn's confession, decides to side with Kitana and free her.
Chapter 10 - Jade
At the Armory, Baraka scolds a fellow Tarkatan for being careless with a gun, and reminds him that they belong to their boss, Shang Tsung. On her way to the Tower, Jade barges in and demands that Baraka step aside so that she can free Kitana. Baraka refuses and challenges her to kombat, where he is consequently defeated. Once she arrives at the Tower, she is met by Sheeva, who tries and fails to stop her from freeing the princess.
Before Kitana can be freed, the two hear their enemies approaching in numbers, and Kitana prompts Jade to leave and seek the help of Raiden. On her way, Jade is cornered by Mileena and forced to subdue her. Jade is then approached by Raiden, Johhny Cage, Kung Lao, Liu Kang and Smoke. Unfortunately, Smoke foolishly confuses Mileena's unconscious body with that of Kitana's and, despite his friends' warnings, blindly attacks Jade in anger. Once their brief scuffle is finished, Jade fills in the group on Kitana's whereabouts, and they send Liu Kang and Kung Lao out to rescue her.
Chapter 11 - Kung Lao
At the Tower, Liu Kang and Kung Lao are ambushed by Sheeva and Noob Saibot. However, as soon as Kung Lao bests Noob, a vengeful Goro approaches. Kung Lao takes down Goro in kombat. Kang and Lao interrogate Goro, who tells them that Kitana is being held at the Coliseum where she is to be executed. With this information, they make their way to the Coliseum.
As they arrive, they find that things are going badly for the Earthrealm warriors. Smoke and Johnny Cage have been defeated, and Sonya and Jax have left Outworld. Shao Kahn challenges Raiden to send in a worthy champion, but Liu Kang, believing that he is not "He [who] must win", refuses to compete and goes to free Kitana instead. Raiden selects Kung Lao in his place. Lao manages to defeat Shang Tsung and Quan Chi in 2-on-1 kombat. Kintaro then make his way to battlefield, but Lao defeats him as well. Celebrating his victory, an unaware Lao is then killed by Shao Kahn from behind by snapping his neck. An enraged Liu Kang, having already freed Kitana, challenges the Emperor to kombat, and defeats him by punching through his chest, seemingly killing him. Kang is declared the winner of the tournament and, as they mourn Kung Lao, Raiden concludes that Liu Kang was meant to win after all, and that Shao Kahn was the one he was supposed to defeat. Despite this, Raiden's amulet cracks even further.
Back in Shao Kahn's throne room, his minions discuss who should take his place. With the aid of Quan Chi's sorcery, however, Shao Kahn survives his injuries. Quan Chi also makes a new proposal to him - a direct invasion of Earthrealm. This by itself is not possible due to the wards that the Queen of Edenia, Sindel, set upon Earthrealm when she committed suicide. Quan Chi is able to overcome this by resurrecting her, imbuing her with full loyalty to the Emperor. With the wards broken, Outworld begins a full-scale invasion of Earthrealm, overwhelming the conventional military forces of Earthrealm.
Chapter 12 - Stryker
During the invasion, police officers Kurtis Stryker and Kabal are among those fighting a losing battle against Outworld's forces. Reptile attacks them on the rooftops, but Stryker manages to fight him off. Both men make their way to a street, where they encounter and defeat Mileena. Stryker and Kabal then watch a fight between Johnny Cage and Motaro from afar, which is interrupted by Raiden, who proceeds to kill Motaro to prevent Cage's foreseen death. Kintaro then appears and seriously burns Kabal with a blast of fire. After Stryker defeats Kintaro, Ermac appears and uses his powers to throw Stryker into a nearby Subway. Stryker defeats Ermac and reluctantly agrees to join Raiden and the other Earthrealm warriors after Nightwolf finds him and informs him of the situation. When he returns to where Kabal was, Stryker finds him gone.
Chapter 13 - Kabal
The scene cuts to the viewpoint of Kabal, who awakens in the Outworld, where Kano has revived him using Shang Tsung's magic and a respirator he created himself. Kano tells him that with his new upgrades, Kabal can serve the Black Dragon again. He also confesses to selling weapons to Shang Tsung, leading Kabal to blame Kano for the Outworld attack. Kabal further insists that he has renounced crime and, after besting Kano in kombat, demands that Kano take him to Shao Kahn. There, they witness Shao Kahn promoting Sindel to general of his army after Motaro's death as she volunteers for the position.
Kahn drains Shang Tsung of all his souls, thereby killing him, and channels them into Sindel in order to give her more power. Kabal knocks out Kano using the hilt of his knife and proceed to attack Kahn. However, he is spotted and challenged by Mileena and Noob Saibot. After defeating both Mileena and Noob, Kabal makes an escape through the Earthrealm portal, where he encounters a now-cybernetic Sub-Zero. Kabal defeats the newly transformed Sub-Zero and knocks him unconscious. Afterwards, Sheeva appears and mistakes Kabal for a turncoat Lin Kuei cyborg. She attacks him, but is defeated. Then, Raiden arrives to invite him to join the other Earthrealm warriors, who have taken refuge in a nearby church.
Chapter 14 - Cyber Sub-Zero
At Smoke's insistence, Cyber Sub-Zero is brought to the Earthrealm warriors, after which Jax restores his free will by reprogramming him. Sub-Zero awakens and expresses guilt over what he had unintentionally done for Shao Kahn. Stryker suggests that Sub-Zero should return to Outworld undercover, to which Sub-Zero agrees.
Sektor, however, notices that Sub-Zero has been reprogrammed and takes him back to Earthrealm. With his cover blown, Sub-Zero attacks Sektor, initiating a duel between them. After subduing Sektor, Sub-Zero hacks into his database and learns that Kano, Goro, and Kintaro have captured some soldiers at a clock tower, and goes to investigate. There, still undercover, he freezes Kano, Goro, and Kintaro, then helps the soldiers escape by breaking their chain. The two Shokan however, free themselves from Sub-Zero's ice, forcing him to knock them both unconscious. However, the soldiers are thrown back to the room by a mystic green aura, with Ermac showing up himself thereafter. Sub-Zero and Ermac engage each other in a rematch, with Sub-Zero wins the second time, thus freeing the soldiers.
The soldiers inform Sub-Zero that they were to be taken to a cemetery, and he makes his way there. He then discovers Quan Chi preparing a spell to create a soulnado. Sub-Zero is soon confronted by Noob Saibot, who reveals to him that he is in fact his late brother Bi-Han, the original Sub-Zero resurrected by Quan Chi, but promptly agrees to relinquish all former family ties. Sub-Zero manages to defeat his brother, but is unable to prevent Quan Chi from completing his spell.
Chapter 15 - Nightwolf
Nightwolf arrives to help, defeats Quan Chi, and knocks Noob into the soulnado, seemingly killing him in the process and destroying the soulnado as well. Nightwolf returns to the church and informs the others that Earthrealm's souls are now safe. To Raiden's frustration, his amulet cracks further. In response, he and Liu Kang decide to appeal to the Elder Gods. As they leave, however, the rest of the Earthrealm warriors are ambushed by the Lin Kuei. There, Nightwolf beats Cyrax in a fight and goes to help Smoke, who is defeated by Sektor.
After they defeat the Lin Kuei cyborgs with relative ease, Kitana senses her mother is coming. Suddenly Sindel appears, stating that she will finish what the Lin Kuei can't. Nightwolf tells his team to attack Sindel, but they are overwhelmed by a newly empowered Sindel. She single-handedly kills Kabal, Stryker, Cyber Sub-Zero, Jax, Smoke, and Jade, and severely injures Nightwolf, Johnny Cage, Sonya, and Kitana. Before Sindel can finish off her own daughter, Nightwolf challenges her to a duel. Nightwolf emerges victorious over Sindel, but his victory is short-lived, as Sindel quickly overpowers him again.
Meanwhile, Raiden and Liu Kang try to convince the Elder Gods to intervene, but the Elder Gods refuse, stating that Shao Kahn has not broken any rules and that invasion of another realm by itself is not a violation. Having achieved nothing, Raiden and Liu Kang return to Earthrealm just in time to witness Nightwolf sacrificing himself to kill Sindel. Sonya and Johnny manage to recover, but Kitana succumbs to her injuries and dies in Liu Kang's arms.
Chapter 16 - Raiden
The now-desperate Raiden decides to form an alliance with Quan Chi, but is forced to go alone after a grieving Liu Kang, who is disillusioned with Raiden and believes him to have gone mad, refuses to come along. As Liu Kang tends to Cage and Sonya, Raiden travels to the Netherrealm and, after fighting off Scorpion, confronts Quan Chi, offering him the souls of all the fallen warriors, including his own, in exchange for his cooperation. However, Raiden soon realizes that Quan Chi has already obtained all the souls of the Earthrealm casualties (Kung Lao, Smoke, Sub-Zero, Jax, Kitana, Nightwolf, Jade, Kabal, Sindel, and Stryker) as part of his deal with Shao Kahn, and sets them on Raiden. Raiden beats Jax, Stryker, Kabal, Kitana, Nightwolf and Kung Lao.
After the fights, the brief discussion with Quan Chi reveals to Raiden that "He must win" in fact refers to Shao Kahn - if he is allowed to merge Earthrealm and Outworld without ten consecutive victories in Mortal Kombat, he will have violated the rules set by the Elder Gods and be punished. Raiden quickly returns to Earthrealm to find that the merger is nearly complete. He explains to Liu Kang that they must allow Shao Kahn to merge the realms, but Liu Kang does not believe this and tries to attack Shao Kahn prematurely, forcing Raiden to fight him.
Liu Kang, infuriated by Raiden's actions, attempts to kill him, but Raiden creates a shield of electricity in defense. Unfortunately, when Liu Kang's fiery fist makes contact, it inadvertently causes a backlash, electrifying and burning Liu Kang at the same time, much to Raiden's horror. Raiden begs Liu Kang to forgive him, who replies, "You...have killed us...all..." before succumbing to his wounds. Cage and Sonya show up and attempt to defeat Shao Kahn together, but are quickly incapacitated. Raiden, realizing there is nothing more he can do to stop Shao Kahn, surrenders himself. Shao Kahn beats Raiden into submission in the same way his future self did, but before he can land the killing blow, the Elder Gods possess Raiden's body. Infused with their power, Raiden battles and defeats Shao Kahn.
- Revenant Jax, Revenant Stryker and Revenant Kabal
- Revenant Kitana, Revenant Nightwolf and Revenant Kung Lao
- Liu Kang
- Shao Kahn
The Elder Gods then attack Kahn and destroy him as punishment for breaking the rules of Mortal Kombat before returning to the heavens. Earthrealm is returned to normal and the cracks in Raiden's amulet disappear, signaling that he has, at long last, prevented Armageddon. After grieving over the massive casualties in the aftermath, Raiden decides to help restore Earthrealm and teleports himself, Cage, Sonya, and Liu Kang's body away.
Later, Quan Chi is revealed to have been acting on the orders of his master, the fallen Elder God Shinnok, the whole time. With both Earthrealm and Outworld severely weakened and a collection of powerful revenants, Shinnok declares that he will soon be free and that both realms will be theirs, foreshadowing events that would take place 25 years later...
- All 16 played characters are fought as opponents at least once throughout the Story Mode.
- Bi-Han is the most frequently fought opponent in the series, as he is fought six times. One of these fights, however, is Shang Tsung assuming his form. He is fought in two different forms.
- As Sub-Zero, he is fought by Sonya, Scorpion, and Smoke.
- As Noob Saibot, he is fought by Kung Lao, Kabal, and Cyber Sub-Zero.
- Kuai Liang is the most frequently played fighter in Story Mode, fighting 4 times as Sub-Zero and 4 times as Cyber Sub-Zero. Liu Kang follows as the second most played, fighting 5 times in Chapter 5 and once in Chapter 11.
- In Kitana's chapter, after defeating Sheeva her unconscious body is shown on the ground, but upon closer inspection, one can see Sheeva is in her alternate costume and not her primary costume
- In Chapter 8, after Kuai Liang was taken away, if listened carefully Shang Tsung mentions the next two combatants are Kenshi and Reiko.
- In Chapter 16, Kung Lao and Stryker as Revenants first appear in their alternate costumes (The ones they died in.). But during the actual fight, they're in their primary costumes.
- Sonya, Scorpion, Liu Kang, Smoke, Kitana, Kung Lao, Kabal, and Cyber Sub-Zero all fight once in which they must deal with two opponents at once. Raiden fights two rounds in which he must fight three opponents at once.
- This is the only Mortal Kombat reboot game to have 16 chapter while the other two games have 12 chapters.
- There are some "rematches" played in Story Mode:
- Scorpion and Sub-Zero fight each other in Chapters 3 and 8. In Chapter 3, Sub-Zero is played by Bi-Han, while in Chapter 8, Sub-Zero is played by Kuai Liang.
- Smoke and Kitana fight each other in Chapters 7 and 9. In Chapter 9, Smoke is teaming up with Johnny Cage.
- Kuai Liang and Ermac fight each other in Chapter 8 and 14. In Chapter 8, Kuai Liang is in his human form. In Chapter 14, Kuai Liang is in cyber form.