For Tower Mode endings, click here
In the events of Mortal Kombat X, the fallen Elder God and ruler of the Netherrealm, Shinnok, waged war against Earthrealm. He managed to succeed in absorbing the realm's life force, the Jinsei, for a time, corrupting it and threatening to completely destroy the world. Earthrealm's protector, Raiden, managed to undo the damage, but in cleansing the Jinsei of Shinnok's taint, wound up subtly influenced by it...
Now wearing Shinnok's amulet as a trophy, an unfettered Raiden holds a defeated Shinnok in the Jinsei chamber, torturing him while stating his intent to no longer simply wait for Earthrealm to come under attack again, but rather, to destroy Earthrealm's enemies preemptively, including Shinnok. Shinnok taunts Raiden with the fact that, as an Elder God, he cannot die.
"There are fates worse than death." Raiden snaps back before decapitating Shinnok, with plans to present his still-living head to Liu Kang as a warning to the Netherrealm of the reprisals to come.
After Raiden teleports away, another presence enters the chamber, approaching Shinnok's head as she mused on how history has gone awry due to Raiden's interference, but all would be set right: "It is only a matter...of time..."
Back in Earthrealm, Cassie Cage is given a promotion to Commander in the Special Forces, a rank that she earns after besting her superior officer and mother, Sonya Blade, in single kombat. The joyous occasion is cut short by the appearance of Raiden with important news: the Netherrealm is amassing its forces. Cassie wants to negotiate with Liu Kang and Kitana, appealing to their former humanity and the fact that they were once allies of Earthrealm. Raiden, however, states that Shinnok's dark magic has eroded away any goodness they may have. The only option, he states, is a preemptive attack on Netherrealm. To that end, he proposes destroying their castle, containing the source of the Netherrealm army's power; the Cathedral of Shinnok, where the necromantic forces' source of power, Shinnok's severed head, lies. Without it, the army would fall in a single fell swoop.
The Special Forces make their move on the Netherrealm, with Raiden providing a diversion: even with his powers dulled in the Netherrealm, Shinnok's amulet gives him strength enough to fend himself against Liu Kang's army. Meanwhile, Cassie leads a team, including Sonya and Jacqui Briggs, into the castle to set explosive charges. Within the castle, the team contends with Kitana and Kabal, a former Black Dragon enforcer who was now among Liu Kang's Revenant elites.
Liu Kang joins the fray, burying several SF soldiers, including Sonya, under rubble. After Cassie fights him off, she tries to dig Sonya out. Sonya, however, orders Cassie to evacuate before activating the charges, sacrificing herself so that the castle would be destroyed and the Netherrealm's army would be crippled.
As Cassie returns to her father, Johnny Cage, to deliver the worst news any husband could ever receive, Liu Kang and Kitana find themselves at a loss of how to proceed now that their army was destroyed. It is then that an Elder Goddess appears before them: Kronika, the Keeper of Time, who offers her aid to the Revenants, first by reversing time to rebuild their castle. She then spirits them away to her Keep, where she explains that her efforts to shape history as she saw fit were disrupted by Raiden's interference. That interference, she states, led to Liu Kang and Kitana's deaths...but it need not be so, as Kronika intends to restart time and mold a new history, a better history where Raiden never existed...
Meanwhile, in Outworld, Kotal Kahn oversees the execution of the Kollector, one of Shao Kahn's lieutenants, at the Koliseum. Before Kotal can carry out his sentence, however, a sandstorm suddenly blows through both Outworld and Earthrealm. In Earthrealm, the sandstorm causes Raiden to suddenly disappear as the three warriors of Earthrealm's past emerge: a younger Sonya, Jax, and Johnny Cage. In Outworld, the sandstorm brings yet more kombatants from yore: Liu Kang, Kung Lao, Kitana, and Jade, before their untimely demise, along with Skarlet, Baraka, and Erron Black, Shao Kahn's elite underlings, in addition to a younger Kano. The sandstorm also brings a young Raiden, before he laid claim to Shinnok's amulet...and Shao Kahn himself!
Shao Kahn, enraged to find his General had taken his throne, engages Kotal in Mortal Kombat. As Liu Kang fights of Shao Kahn, Baraka confronts Kotal, the Osh-Tekk and Tarkatan peoples having a long and sordid history before the Tarkatans' extinction in the present era. After fending of Baraka, he is ambushed by Skarlet, an orphan whom Shao Kahn took under his wing and taught blood magic, ensuring her loyalty.
After defeating Skarlet, Kotal is reunited with Jade, his lover. Their reunion is interrupted by Erron Black, whose past self never allied with Kotal. Defeating him is a trivial matter, and Kotal goes to fight Shao Kahn once more.
Before Kotal can put Shao Kahn down, the tyrant is rescued by D'Vorah, who helps the other Outworld warriors of the past escape. With his enemies retreated, Kotal discusses the matter with Raiden, whose present-day counterpart was an enemy who was tainted by Shinnok's amulet into becoming a viscious tyrant. The younger Raiden proposes an alliance in order to overcome a common threat, to which Kotal agrees.
In D'Vorah's hive, the Kytinn queen catches Shao Kahn up on events that transpired since his death, including the death of his daughter Mileena by her own had and Kotal's subsequent ascension to the throne. Shao Kahn is enraged at D'Vorah, but his hand is stayed by the appearance of Kronika, who requests Shao Kahn's aid in helping her reshape history in exchange for a greater empire, and more importantly, no Raiden. Shao Kahn readily agrees to aid her.
Meanwhile, back in Earthrealm, as Johnny realizes just how much of an asshole he was in his younger days, Cassie becomes acquainted with her mother from decades prior, as does Jacqui and her father, whose present self had fallen into depression after his experiences as a Revenant and the death of his wife. Raiden, troubled by what he learns of his future self, learns that Netherrealm's supposedly routed army was seen at the Shaolin Temple. They are likely moving on the Dragon Grotto, a place where the essence of the Jinsei, Earthrealm's lifeforce, flowed in the waters. If Kronika had the power of the Jinsei, the danger she posed would become greater still. To this end, Raiden sends Liu Kang and Kung Lao to the Shaolin Temple to stop her.
While making their way to the temple, Liu Kang and Kung Lao discuss their troubling futures as Revenants. Kung Lao is worried that if they continue to follow Raiden, the same fate will befall them. Liu Kang, however, is resolute in his trust in the Thunder God.
Within the temple, the two encounter the past Scorpion, the Revenant ninja consumed by vengeance. They fight him off, only to find themselves trapped in a cage as poison gas fills the temple. The gas suddenly subsides, however, as Scorpion returns with the present Revenant Jade in tow. She, too, is fended off.
As Raiden entreats the Elder Gods for their advice, Liu Kang and Kung Lao make their way to the Dragon Grotto, finding Geras, Kronika's top enforcer, collecting vials of Jinsei-enfused water. Their future Revenant selves emerge to keep them from stopping Geras, warning them that they would end up exactly like them if they continued to follow Raiden. The past Shaolin monks manage to fend off their future selves before engaging Geras, but in spite of their best efforts, Geras is able to reverse any damage inflicted upon himself.
The two monks try to reclaim the vials, but are stopped by Geras's time-altering powers as Kronika emerges. Geras questions whether it's wise to keep them alive. Kronika explains that their survival is key; without them, their future Revenant selves would cease to exist, and they are instrumental to her plan.
With the Jinsei, Kronika's plan to rewrite history proceeds. Shao Kahn promises to have his Outworld army ready to protect her Keep once he disposes of Kotal. Her defenses would be further bolstered by the resurrected Cyber Lin-Kuei, courtesy of Sektor...
Raiden returns from his meeting with the Elder Gods, informing Liu Kang and Kung Lao that they may yet thwart Kronika's schemes if they can find her Keep. Kung Lao remains troubled at the fact that, in the future, Raiden played a part in their deaths, but Raiden assures him that their destiny may yet change if they succeed in stopping Kronika.
In the meantime, the Special Forces discover that Sektor has returned, and several Lin Kuei have gone missing. In addition, an old Cyber Lin Kuei factory has been restored, likely thanks to Kronika.
Two assassins make their way to the Cyber Lin Kuei factory. They are the grandmasters of the Shirai Ryu and the Lin Kuei: Hanzo Hasashi and Kuai-Liang, also known as Scorpion and Sub-Zero. Once hated enemies, the two grandmasters and their clans now united against a common threat.
Kuai-Liang has an idea on how to deal with the Cyber Lin Kuei: they would infiltrate the factory and enlist the aid of someone on the inside. While infiltrating the factory, Kuai-Liang finds several bodies of his fellow Lin Kuei mutilated, troubling him greatly. They soon find their intended ally: Cyrax, a Lin Kuei who was cyberized against his will. If Kuai Liang can remove his behavioral inhibitors and restore his free will, Cyrax could help them shut down the Cyber Lin Kuei.
The two make their move to liberate Cyrax, only to be confronted by a old enemy: Frost, a female cryomancer who betrayed Sub-Zero her own grab for power. The two eventually manage to chase of Frost and subdue Cyrax. They are then ambushed by Noob Saibot, the shadowy Revenant of Bi-Han: Kuai-Liang's elder brother who held the title of "Sub-Zero" before him. After fending Noob off, the two succeed in restoring Cyrax's free will. As he offers his aid, however, Sektor attacks them.
With Sektor defeated, the Grandmasters and Cyrax can shut down the Cyber Lin Kuei. Beforehand, Cyrax beseeches Sub-Zero to find a way to restore his humanity. Kuai-Liang, who knows all too well what it's like to be robbed of his humanity, assures Cyrax that man or machine, he still has his soul, and he would always be welcome in the Lin Kuei. With that, Cyrax shuts down the Cyber Lin Kuei, including himself.
As the Cyber Lin Kuei factory is shut down, Kronika takes Sektor's chassis back to her keep, in the hopes that Erron Black and the younger Kano can repair him and use him to mass-produce her own cybernetic army. The present incarnation of Kano appears to sweeten the deal: in Kronika's new history, the Black Dragon clan would reign supreme over Earthrealm.
Back in Earthrealm, Jacqui tries to contact her father, but to no avail: the SF's communication network is down. Jax, himself, stresses over the welfare of his daughter. That night, Kronika approaches him, stating that history should not have been so cruel as to see his daughter pressed into military service. He should have grandchildren by now...if he helps Kronika, she may set things right for him...
In Outworld, Raiden discusses how to proceed in Outworld with Kotal Kahn and Jade. If D'Vorah had brought Shao Kahn back to her hive, that would be where they would commence their search for him while Raiden sought further advice from the Elder Gods. Meanwhile, Kotal asks Kitana to speak with the leader of the Shokan, Sheeva, and request her aid: a tall order, considering the Osh-Tekk's bad blood with the Shokan, but nonetheless aid they desperately need.
As they march on D'Vorah's hive, Jade discusses how history transpired since her death in the present timeline with Kotal. Kotal reveals that even after becoming Kahn, he never took an empress, for none could replace Jade in his heart.
Upon reaching the hive, Kotal orders his forces to set it aflame. Before they can, however, giant spiders drag Jade into the hive, where she is confronted by her future Revenant self, warning her that her loyalty to Kitana was her undoing. Undeterred, Jade fights off her future self. Kotal appears afterwards, with D'Vorah in pursuit. As D'Vorah prepares to kill Kotal, Jade intercedes and forces her to give up Shao Kahn's location.
This leads Jade and Kotal to a Tarkatan village. Jade sneaks into the village to try and find Shao Kahn, but is discovered and pursued by the Tarkatan soldiers. She is confronted by the Kollector, whom she fends off with ease.
Kotal joins into the fray and orders executions of several Tarkatans, several innocent women and children. Jade beseeches Kotal to reconsider, but the present Kahn is resolute in carrying out his judgment. Disturbed at how hardened her love's heart had grown, she fights and defeats him before Shao Kahn captures them.
Meanwhile, Raiden returns to the realm of the Elder Gods, only to find them gone, all except for Cetrion, who reveals that she is Kronika's daughter, and Shinnok, her brother. Kronika's plan would restore the balance of light and darkness in the realms, with Cetrion counterbalancing Shinnok's darkness with her own powers of light. The other Elder Gods opposed Kronika's plan, so Cetrion betrayed them. Raiden's interference had disrupted this balance so badly that Kronika's New Era mandates he no longer exist. With Kotal captured, history hangs ever more precariously in the balance...
All the while, back in Earthrealm, the past Jax learns of the troubling fate that befell his future self. After returning from being a Revenant, the present-day Jax was racked with guilt. He found solace in the love of the woman who helped nurse him back to help, whom he would marry and have Jacqui with...and who, sadly, died last year, causing him to spiral...
Back in Earthrealm, Cassie helps Sonya catch up with everything that transpired in the future as the Johnny Cages admire her. The younger Johnny Cage is rather crass about the fact that, eventually, he and Sonya become an item, drawing the elder Cage's ire and leaving Sonya wondering how she ever fell in love with Johnny. The elder Cage tries to talk sense into his younger self, but the past Johnny continues to act belligerent until the past movie star and the present-day family man come to blows.
As Sonya learns that Cassie had left her future self behind to die and confronts her daughter, Kronika's forces begin to lay siege to the SF base, led by the past and present Kanos with Erron Black, a rebuilt and reactivated Sektor, and an army of Cyber Lin Kuei in tow. In the fighting that breaks out, the past Cage has a bullet graze his cheek, causing a scar to appear on his future self's face in the exact same spot...
As the past Johnny charges off, the present Cage confronts Erron Black, whose past self was allied with the Black Dragon clan. After dispatching him, Cage finds Cassie injured, but otherwise in one piece. Unfortunately, Sonya was abducted in the melee.
Cage gives chase after Kronika's army, using an SF tank to down an aircraft intended to extract her forces. He then contends with Sektor and the past Kano. Unfortunately, the present Kano manages to capture the past Johnny and holds him at gunpoint, warning him that if anything were to happen to the past Johnny or Sonya, Cassie would never be born. The Kanos leave with their hostages while triggering Sektor's self-destruct sequence, forcing Earthrealm's heroes and Raiden to escape to the Shirai Ryu's headquarters, the Fire Garden, where Hanzo offers them shelter. Thankfully, Cassie managed to place a tracking device on one of Kronika's jets beforehand. The situation remains dire with the Elder Gods vanquished, however. Their only hope lies in Kotal Kahn's survival and Outworld's willingness to help...
Kitana gains an audience with Sheeva and asks for the Shokan's help. Sheeva, however, is not willing to throw her lot in with her people's nemesis without the Tarkatans also willing to help. Kitana vows to rescue Kotal and gain the Tarkatans' support.
Liu Kang and Kung Lao infiltrate the Tarkatans' village, posing as Outworlders who had captured Kitana. Skarlet, however, manages to see through their deception and attacks. Kitana fends of Skarlet, rescuing Jade in the process. Before they can move on the Koliseum, where Shao Kahn intends to execute Kotal, Baraka confronts Kitana, having no intention of siding with the Osh-Tekk who would kill his people. Kitana manages to defeat Baraka, however, and beseeches him to help them defeat Shao Kahn, a konquerer whose konquests never benefited the Tarkatans. Never before has anyone thought to ask the Tarkatans for their aid. Baraka would be willing to help Kotal, but only if the Kahn, himself, asks for his aid.
At the Koliseum, Shao Kahn prepares to execute Kotal, but Kitana and her allies arrive to stop him. After fending off the Kollector, she fights Shao Kahn in Mortal Kombat, emerges victorious, and kills the tyrant who robbed her of her homeland of Edenia. Unfortunately, Kotal would up being paralyzed by Shao Kahn beforehand. No longer in any position to lead, he passes rule of Outworld to another who is worthy: Kitana Kahn. Kitana readily agrees to lead Outworld against Kronika, winning the allegiance of both the Tarkatans and Shokan in so doing.
Back in Earthrealm, the location of Kronika's Keep remains as elusive as ever. Hanzo, however, knows of someone who could possibly be of help from his time as a Revenant: Kharon, captain of a ship that ferried the souls of the damned to the Netherrealm. Kharon could travel between the realms, and would be the one in the best position to find the Keep. Hanzo and Kuai-Liang leave to find Kharon while Liu Kang and Kung Lao rally the Shaolin monks.
There is still the matter of Kronika's next move. With the Jinsei no longer accessable to her, she would need a new source of power to advance her agenda. Such an energy source does exist in Earthrealm: the Well of Souls on Shang Tsung's island. As Jax and Jacqui prepare to move on Shang Tsung's island, Cassie prepares to mount a rescue mission for the past Johnny and Sonya...
Sonya awakens to find herself in an underground fight club, trapped in a dingy arena as the Kanos look on and taunt her. They first pit her against the past Kabal, fed on lies of how Sonya was responsible for his future mutilation. After fending off the speedy Black Dragon enforcer, they then pit her against an injured past Johnny, threatening to kill them both unless they fight for the crowd's amusement. Sonya and Johnny both know the Kanos plan to kill them regardless, but Sonya reluctantly agrees to punch Johnny while they come up with a plan of escape.
Thankfully, the Special Forces, led by Cassie, manage to break them free. Erron Black prepares to kill the past Johnny, but Sonya manages to chase him off. The fight spills outside, where Sonya confronts the past Kano, noticing how her attacks affected his future self. After subduing the past Kano, the present Kano holds the past Johnny at knifepoint and threatens to kill him, erasing Cassie from existence. After sarcastically thanking him for reminding her of "the rules", Sonya pulls a gun and blows the past Kano's brains out. The present Kano suddenly finds himself with a gaping hole in his head before he fades away into nothing, his body dissolving like sand in the wind.
As Sonya finally begins to realize the past Johnny isn't so bad a guy, Geras appears and goes on the offensive. Every attempt to kill him ends in failure until Cassie pins him to the wall with a forklift and blows him to pieces with some grenades. With Geras indisposed, Sonya has the chance to apologize for going off on Cassie before, having since learned that her future self had ordered Cassie to leave her behind, sacrificing herself to their mission could succeed and Cassie could live. Their relief is shortlived, however, as Geras's body begins to reconstitute itself, forcing the Special Forces into retreat.
Back in Kronika's keep, news arrives of Geras's defeat, Shao Kahn's death, and the Outworld army changes sides. Kronika, however, has another ace up her sleeve; the Well of Souls on Shang Tsung's island. A single soul contains an immense amount of power, so the Well of Souls would provide more than enough energy needed to see her plans through.
Elsewhere in Earthrealm, Jacqui and Jax make their way to Shang Tsung's island, Jax's mind feeling a bit at ease knowing how his future plays out after having been thrust headlong into the supernatural since losing his arms to Ermac, as well as a conviction to see the future play out better for his future self. Upon arriving on the island, the future father and daughter duo find themselves confronted by the Revenant Jade and Kabal, both of whom are easily fought off.
Deeper into the island, they confront Noob and chase him off before finding the Well of Souls, and within it, Kronika's crown. As they prepare to leave with it, however, the present Jax confronts them, his cybernetic arms rebuilt by Kronika, with whom he allied out of a hope for a better future for Jacqui in the New Era. The past Jax confronts his misguided future self.
After incapacitating the present Jax, the past Jax and Jacqui get ready to leave, but are confronted by Cetrion, who demands Kronika's crown. The duo use the crown's power to fight Cetrion on equal footing, but wearing it proves taxing to them, and fails to defeat her. With the present Jax awake again, Cetrion creates a fissure in the ground, with Jacqui holding on to dear life as Cetrion demands the crown, threatening to kill Jacqui otherwise. The present Jax, unwilling to let his future daughter die, relinquishes the crown. Cetrion brings Jacqui back up as she and the present Jax leave.
With the empowered crown now in her hands, Kronika's plan enters its final stages. The situation has grown increasingly dire, such that Cassie begins to think Raiden should use Shinnok's amulet to even the odds. Raiden, however, is unwilling to let himself fall under its evil influence. If Hanzo and Kuai-Liang cannot get Kharon's aid, all hope is lost...
In the Netherrealm, Hanzo and Kuai-Liang notice how Cetrion is constructing a bridge to help her army traverse, even though doing so taxes her powers to their limits. It would be far easier to force Kharon to help her, but the fleet only moves by Kharon's will. If his fleet is still ashore, it means that he has refused to aid Kronika. Hanzo advises Kuai-Liang to return to Earthrealm while he looks for Kharon.
Hanzo finds Kharon as D'Vorah's prisoner and fends her off, only to be confronted by his past self. The past Scorpion calls Hanzo's revived Shirai Ryu out as mere pretenders; with his family dead, the Shirai Ryu, as far as Scorpion is concerned, is no more. Hanzo manages to defeat his past self, and explains to him how Kronika is manipulating his anger at the death of his wife and child, just as Quan Chi had. He asks Scorpion for help, but is ambushed and fatally poisoned by D'Vorah. Scorpion chases off D'Vorah, but Hanzo is quickly dying. He explains how what's important to the Shirai Ryu is not blood, but the heart of those in it, and beseeches his younger self with his dying breath to help Raiden protect Earthrealm.
Moved by his future self's words, Scorpion returns to Earthrealm to offer his aid to Raiden. Kuai Liang is suspicious of the past Scorpion and confronts him, but Raiden refuses to trust him...
Liu Kang begins to think there may be truth to Scorpion's request to help Raiden, but the Thunder God has fallen deaf to reason: he had taken Shinnok's amulet, and its dark influence was driving him to become increasingly viscous and heartless. Liu Kang begins to believe Kung Lao's own suspicions were spot on: that Raiden couldn't be trusted after all! "If you must die, so be it!" Liu Kang cries.
Those words cause Raiden to come to a frightening realization: this has happened before! He recalls earlier in this timeline how he sought to defeat Shao Kahn during his attempt to forcibly merge Earthrealm and Outworld by allowing the merger to happen and forcing the Elder Gods to intercede. Liu Kang had thought Raiden to have gone mad, declaring "If you must die, so be it!", and fighting his former mentor. These events didn't just play out in this timeline, either, but in countless timelines before, every one seeing Raiden and Liu Kang forced into kombat against each other, all thanks to Kronika's manipulations!
Discarding Shinnok's amulet, Raiden comes to his senses, apologizing to Scorpion and accepting his help as Kronika appears to taunt Raiden. She explains that the combined might of Raiden and Liu Kang was the biggest threat to her plans. She welcomes Raiden to try and stop her, but abducts Liu Kang before taking her leave.
Liu Kang's capture forces Raiden to proceed immediately with the assault on Kronika's Keep. Kharon leads the fleet, carrying the Shaolin Monks, the combined armies out Outworld, and the Special Forces. They are met by Kronika's battleship along the way, with the present Jax confronting Raiden. After besting him, Raiden explains to Jax how Kronika manipulated him, being the mother of the same fallen Elder God that turned him into a Revenant. Realizing the error of his ways, Jax allies with Raiden once more against Kronika.
Geras then confronts Raiden, assured that his immortality would allow him to win. Raiden, however, manages to defeat him, pinning him down with chains tied to a dropping anchor. Geras taunts Raiden with the fact that he can never drown, but such was not Raiden's plan; the bloody oceans of the Netherrealm were bottomless, and Geras would be continuously pulled deeper and deeper into its infinite depths for the rest of time.
Frost then attacks Raiden. After Raiden defeats her, he and Sub-Zero discover that it was Frost, not Sektor, who led the Cyber Lin Kuei. With the Cyber Lin Kuei's collective consciousness linked to Frost's mind, Raiden puts her out of her misery by short-circuiting her control over her robotic minions, defeating the cyberized assassins once and for all.
As Kronika's Keep comes into view, the Revenant Liu Kang attack Raiden, having used dark magic to suck out the soul of his past self and increase his strength. Raiden, however, manages to emerge victorious, stating that he conquered his inner darkness, and that Liu Kang must do so as well.
"You will have to kill me!" Liu Kang snaps.
"I would rather save you..." Raiden says quietly before placing his energized hands to Liu Kang. The past Liu Kang suddenly comes to life for a moment before vanishing as Raiden and the present Liu Kang are enveloped in divine light...
When the light fades, Raiden is nowhere to be seen. Liu Kang now stands, his life restored, his hair white, and his arms adorned in glowing tattoos. Raiden had merged his life force with Liu Kang, turning him into a demigod. He also had his Revenant self's knowledge of Kronika's plan and her keep.
With Liu Kang and Raiden now merged, Kronika's plot has been jeopardized, forcing her to proceed with greater haste as the Earthrealm and Outworld armies march on her Keep. Liu Kang charges ahead into the Keep with Kung Lao and Kitana Kahn at his side. By the time they find Kronika, however, they are too late: Kronika begins to rewind the sand in her Hourglass, reversing the flow of time. With Kung Lao and Kitana no longer at his side, Liu Kang is forced to fight the Revenants of Kung Lao, Kitana, and Jade by himself. Cetrion joins the fray afterwards, but Liu Kang defeats her.
Kronika then absorbs Cetrion's life force, giving her the power she needs to finish the reversal of time. She begins to wind back the clock much more rapidly...
Liu Kang finds himself at the beginning of time. The friends he made, the rivals he faced, everyone he ever knew no longer existed. His history is completely undone. All that is left for Kronika is to kill Liu Kang: he had become an immutable obstacle, and thus no longer had any place in Kronika's New Era.
Liu Kang, however, manages to emerge victorious, his Jinsei-empowered flames fusing the grains of sand forming Kronika's body into glass that shatters easily with a light blow.
With Kronika dead, Raiden appears once more: now a mere mortal, no longer the God of Thunder. Liu Kang had proven himself worthy to succeed him as the restored Earthrealm's protector. The responsibility of reshaping history now falls to Liu Kang, a monumental task, but one that Raiden pledges to aid him for as long as he may live
"Then together, let us begin." Liu Kang says, turning to the Hourglass to set about the task of rebuilding the realms...
However, Liu Kang manages to stop Kronika before she can turn back time too far, fusing the grains of sand comprising her body into glass and shattering her with a glancing blow. With Kronika dead, Raiden appears once more, no longer Earthrealm's guardian god. The responsibility for protecting Earthrealm now falls to Liu Kang, as does the responsibility of using the Sands of Time to start a new, better timeline. It is a monumental task, one which Liu Kang cannot hope to complete by himself...but thankfully, time had not wound back so far that he could not illicit aid from one whose fate was forever intertwined with his own: Kitana.
After saying his farewells to Raiden, Liu Kang returns history to the dawn of time, with Kitana at his side. Although there is a chance that this new timeline may not be ideal, as mortals will make their own choices, and new evils will emerge. Liu Kang resolves to, nonetheless, face what comes...
Liu Kang is powerless to stop Kronika. Just as Raiden had done to her son Shinnok, Kronika decapitates Liu Kang, removing the last obstacle to her grand design as she declares: "Let the New Era.....begin!"
Shang Tsung warns that attempting to start history over would doom all realms: Kronika could only control the Hourglass with her crown, which had been destroyed when Liu Kang destroyed her. Without the crown, attempting to manipulate the sands of time would only destroy the Hourglass, destroying reality outright. To Raiden's surprise, even Fujin concurs! Nightwolf explained that Kronika had approached them in helping her forge her New Era, and when they refused, banished them into a Void beyond time that left them powerless to intercede. When Kronika was killed, Shang Tsung was able to break himself and his fellow prisoners free of the Void.
To save history from being completely undone, Shang Tsung proposes going back in time to retrieve Kronika's Crown. At one point, Shang Tsung had the Crown on his island. If he could steal it away before Cetrion could take it, there is a chance the realms could yet be saved. Shang Tsung knows all this because Kronika had him born for the sole purpose of fashioning her crown from the countless souls he took: the reason he chose not to side with her is because he refuses to be anyone's servant, least of all hers. Raiden refuses to trust Shang Tsung, but even he cannot argue that the deadly alliance he is proposing is their only option.
While Raiden and Shang Tsung argue, Liu Kang and Fujin discuss a matter in private. Afterwards, Liu Kang agrees with Shang Tsung's plan to retrieve the crown, sending Fujin and Nightwolf with him to keep an eye on him while he and Raiden remain behind to watch over the Hourglass.
The three make their way into an underground tunnel, only to be confronted by the Kollector, who noticed them trying to slip away. With Shao Kahn offering a kingly sum for Shang Tsung's head, the Kollector plans to claim it. He opens two pens in the tunnel, unleashing a pair of beasts that chase after Shang Tsung and Fujin, leaving Nightwolf to deal with the Kollector. Nightwolf manages to fend off the Kollector while Shang Tsung and Fujin dispose of the beasts. At the same time, Kitana claims victory over Shao Kahn, becoming Outworld's new Kahn in so doing, and giving the three the distraction they need to slip away.
Unfortunately, their appearance in the middle of the melee between Kitana and Shao Kahn has made a direct assault on Shang Tsung's island impossible: Kronika's allies will certainly have noticed and informed her of their arrival, and attempting to go to the island now would only result in them falling by Cetrion's hand. They would need more help if they were to deal with Cetrion, but whose help could they count on without altering the course of the Time Merger's events? Shang Tsung can think of but one: Sindel, who is a Revenant in this timeline and who played no major roles in the Time Merger's events. She could be safely restored to life without disrupting events. Fujin is not convinced that this will be any help: the Sindel of this timeline had killed most of Earthrealm's warriors in a single fight. By restoring her to life, however, Shang Tsung is convinced the mind manipulation that had been placed on her by Quan Chi to make her Shao Kahn's willing wife would be undone. To accomplish this, they would need Earthrealm's Jinsei to undo her death, and Outworld's Soul Chamber to undo Quan Chi's enchantment. Nightwolf, who had sacrificed his life to defeat Sindel, is less than enthusiastic about this plan, but agrees to it for want of another solution.
The three make their way to the Jinsei's grotto, with Fujin staying at the grotto to secure it while Shang Tsung and Nightwolf explore the Shaolin temple. The two are soon confronted by Geras, Frost, and a small army of Cyber Lin Kuei. Nightwolf manages to fend off both Frost and Geras while the others make short work of the Cyber Lin Kuei, then cast Geras away to Chaosrealm while he is trying to recover from his fight with Nightwolf.
The three then make their way to the Netherrealm to search for Sindel. She was not seen in the Revenants' war march, and Shang Tsung recalls that she had been absent during Earthrealm's assault on the Revenant Liu Kang's keep. Before they can discern why, Nightwolf senses his own Revenant's approach, accompanied by the Revenants of Liu Kang and Kitana. The three are subdued and imprisoned in Shinnok's Bone Temple, Sindel's domain. Sindel promises to make Nightwolf suffer in retribution for killing her, but Nightwolf manages to free himself, Fujin, and Shang Tsung. Nightwolf personally confronts Sindel and defeats her, then turns his attention to his Revenant self, who has weakened Shang Tsung. After the Revenant is defeated, Shang Tsung absorbs its soul to recover from his wounds. Nightwolf prepares to stop him, but Fujin forces him to stay his hand: Shang Tsung's must survive if the realms are to be saved.
The three then take Sindel with them to Outworld to entreat Sheeva's aid in reaching the Soul Chamber.
As the four make their way through the Dead Pools, they find themselves confronted by Erron Black and Baraka, the latter of whom is also loyal to Kitana and questions Sheeva's acts in escorting Earthrealmers with a coffin. Shang Tsung had disguised himself as a Shokan, but Baraka sees through his disguise and stabs him. Erron Black aims to take Shang Tsung and the coffin into custody as Baraka and his Tarkatan soldiers go on the attack. Sheeva fights Baraka, herself, then confronts Erron Black.
They are then approached by Jade, to whom Sheeva explains the situation. Jade is not convinced yet, and regardless, Kotal was using the Soul Chamber to recover from having his spine broken. Sheeva is forced to fend off Jade, knocking her unconscious, but leaving her alive.
The four proceed further towards the Soul Chamber, where Kotal is recovering from his injuries. Kotal awakens and sees Shang Tsung, determined to kill him for his captivity in the Flesh Pits, even though his recovery is incomplete. Sheeva tries to explain that they need his help to revive Sindel, but Kotal will not listen: necromancy is a forbidden art, and he cannot abide. Sheeva holds Kotal at bay while Fujin and Shang Tsung set about reviving Sindel.
After subduing Kotal, Kitana confronts Sheeva about her questionable allegiance with Shang Tsung. Refusing to believe any good can come of the sorcerer's ill magic, she moves to stop him, but Sheeva stands between them, her loyalty to Sindel overriding her oath to Kitana.
In the end, Shang Tsung's plan works: the combination of the Soul Chamber's power and the Jinsei's essence breathes life back into Sindel. Sheeva is overjoyed to see Sindel alive again and begs her forgiveness in failing to protect her before, but Sindel assures her that she did enough and more for her by helping to bring her back to life. Kitana is also excited to see Sindel alive, but questions why she killed herself before and abandoned her. Sindel explains that she had actually been murdered by Quan Chi, who staged her death as a suicide. There is little time to celebrate, however: Shang Tsung's island, and the Crown, await. Kitana stays behind in Outworld to continue her work as Kahn while Sindel accompanies Shang Tsung and his allies.
In her keep, Kronika observes Sindel's resurrection. As Sindel can potentially derail her plans, her hand is forced: she orders Cetrion to immediately make for Shang Tsung's island and retrieve the Crown.
Fujin fights and fends off Kabal, while the others subdue Jade and rout the zombies. Sindel and Nightwolf volunteer to remain behind and fend off any other pursuers while Shang Tsung and Fujin make their way towards the Crown. As Fujin ponders how long it will be until Shang Tsung betrays them, they reach the Crown. Unfortunately, they are not alone: Jax, who had been coaxed to aid Kronika with the hopes of a better future, confronts them, along with Noob Saibot.
As Fujin feds off Noob, Shang Tsung starts trying to steal Jax's soul. Fujin stops him, then subdues Jax, trying to explain that Kronika's promises were for naught. Jax shoots back that Fujin couldn't possibly understand what it was like to do whatever it takes, even sell one's soul, for family: he was a god, he could never know. Fujin argues back that he and Raiden once fought when he made the choice to leave the Sky Temple to live amongst humans, with Raiden warning him not to be so attached to something as ephemeral as other mortals. Fujin knows, however, that their strength comes from their bonds with family and loved ones. He then warns Jax that his daughter, Jacqui, was on her way to the island: Kronika hoped to pit them against each other. Surely, Jax can do better than to throw in his lot with someone who cares so little for him and his family.
As Jax begins to come around to Fujin, the ceiling in the Crown's chamber collapses. Sindel, aided by Nightwolf, is fighting a desperate battle against Cetrion, but the Elder Goddess proves to be a challenging opponent. Ultimately, however, Sindel is able to weaken Cetrion enough for Fujin and Shang Tsung to finish her.
Jacqui and the past Jax arrive shortly thereafter, with a squad of Special Forces at their side. The present Jax and Fujin manage to defuse any possible conflict: he has the Crown, and with it, the course of history has been significantly altered. There is no telling what can happen now. All that remains is to present the Crown to Raiden.
Sindel returns to Outworld to aid her daughter, Kitana Kahn, while Nightwolf remains behind with Jacqui and both Jaxes to aid the Special Forces, agreeing to meet again in six hours at the Sea of Blood for the final assault on Kronika.
As Cetrion reports her failure to stop Shang Tsung to Kronika, Shang Tsung and Fujin makes their way to the Shirai-Ryu Fire Gardens and approaches Sub-Zero and the past (yet reformed) version of Scorpion. Fujin asks to meet with the past version of Raiden, but Sub-Zero and Scorpion are not too trusting with the company he keeps. Fujin fends off both Sub-Zero and Scorpion, then approaches the past versions of Raiden and Liu Kang to explain the situation. Raiden refuses to listen to either the sorcerer or his brother whom he believe to be deceived, brandishing Shinnok's amulet. Shang Tsung warns Raiden about the amulet, and Liu Kang tries to convince him to at least heed him and Fujin, but Raiden has become deaf to reason because of the amulet's influence.
Fujin intercedes, and manages to wrest Raiden free from the amulet's influence with Shang Tsung's assistance. Afterwards, Fujin tells Liu Kang of the events to come that lead to his ascension to godhood. Raiden cannot expedite the process, however: he would need to save Liu Kang's Revenant first. Before Fujin can tell anything else about the battle to come, however, everyone except for him, Raiden, and Shang Tsung are frozen as earthen statues by Kronika, who has come to confront them directly. Kronika explains that even though she had been defeated once before, the current timeline's continued existence was indicative of the fact that there was no victory for Raiden or Liu Kang. Kronika warns them that Shang Tsung would betray them. His knowledge of the Crown was because he, himself, created it. As she puts it, history can only be kept safe under her guidance. Raiden, however, is still resolved to defeat her, as well as Shang Tsung, should he betray them.
Kronika places Raiden into stasis, and prepares to do the same to Fujin, threatening to erase him from existence. Fujin, however, dons the Crown himself, resisting Kronika's powers. Together with Shang Tsung and a liberated Raiden, he drives Kronika away. The Crown falls from Fujin's head as he becomes exhausted from using its vast power. Shang Tsung retrieves it and, after taking a moment to admire his craftsmanship, hands it to Raiden.
Afterwards, Sindel makes her way into the dungeons, where she finds Shao Kahn, spared by Kitana, being tortured by Shokan. She disposes of her husband's wardens, then goes to his aid to help him reach the Soul Chamber, restore his health, and wrest the throne of Outworld away from Kitana. Unfortunately, Sheeva overheard her scheme. Sindel defeats Sheeva, then when other Shokan arrive, explains that Kitana murdered Shao Kahn's wardens and brutalized Sheeva, coaxing them to join her in exchange for vengeance.
His vitality restored by the Soul Chamber, Shao Kahn is ready to join Sindel in taking the Hourglass, and the course of history, for themselves. They are then approached by a strengthened Geras, who wants to recruit them into Kronika's army. Shao Kahn refuses, however, as Kronika did nothing to aid him when Kitana usurped Outworld from him.
While Shao Kahn's return to the fold and his betrayal are unexpected, Kronika sees an opportunity in this turn of events: Shao Kahn would fracture the unified forces bound for her keep, and the fight between Raiden and Shao Kahn over the Crown would give her the chance she needs to reclaim it.
After defeating Geras, the terrible twosome sic their newfound army of Shokan on the rear guard of Raiden's army. They are confronted by Cassie Cage and the past Johnny Cage, the latter of whom is enraged at Shao Kahn and Sindel harming the love of his life and their future daughter.
The Cage-Blade family is taken into Shao Kahn's custody as he and his army take the last remaining vessels in the united fleet. They soon overtake the ship carrying Kitana Kahn, Liu Kang, Kotal and Kung Lao, laying siege to their army. After fending off Kung Lao and dealing with Kotal, the two go to confront Kitana and Liu Kang personally. Kitana questions what spell her mother is under, but Sindel explains that she is not under anyone's thrall: in fact, she had grown to resent her first husband, King Jerrod, for being a weak ruler. She welcomed Shao Kahn's konquest, and even helped him kill Jerrod! Kitana lashes out while Liu Kang faces the Emperor for yet another time, but both of them are subdued.
With the armies of Outworld now under Shao Kahn's banner once more, Shao Kahn and Sindel continue on towards Kronika's keep.
Kotal's head is presented to the forces ashore, and Shao Kahn leads the charge. Raiden asks Fujin for the Crown so that he can rout Shao Kahn and Sindel...only for the real Raiden to confront the disguised Shang Tsung, his betrayal now laid bare!
With the Crown now placed upon his head, Shang Tsung's powers are amplified, and his youth restored. With the power of a Titan at his fingertips, not even Raiden and Fujin can hope to best him! The gods of thunder and wind have their souls and the powers taken, leaven them weakened and wizened.
Shao Kahn, pleased to see his nemesis brought to kneel, proposes finishing him. Shang Tsung, however, has a better idea: use them to fuel their powers for time eternal.
Backed into a corner, Kronika sacrifices her daughter Cetrion to absorb her power. When Shang Tsung, Shao Kahn, and Sindel enter her chamber, she sends the Revenants of Kung Lao, Kitana, and Jade to stop them. The Revenants are powerless to stop them, however.
As Shao Kahn gloats over the weakened Kronika, Shang Tsung suddenly betrays him and Sindel, blasting them with fire while declaring he, himself, would kill Kronika while they would serve him. Shao Kahn refuses to be anyone's servant, but neither he nor Sindel can stop Shang Tsung, who easily defeats them and takes their souls.
Kronika, having regained her strength, confronts Shang Tsung, who makes her an offer: serve him, or be erased from history. Kronika fights Shang Tsung, but is soundly defeated, the Titan's soul absorbed by the sorcerer. With none left to oppose him, Shang Tsung prepares to sculpt the sands of the Hourglass to create a new history, in which he reigns eternal.
Shang Tsung is then confronted by the future Fire God Liu Kang, who warns him to stop. Shang Tsung questions why he would come when the sands of time in the future require his supervision, but Liu Kang reveals that was a lie, one Shang Tsung had ironically fallen for. Shang Tsung realizes that Liu Kang had allowed him to win against Kronika by taking the Crown, sacrificing the lives of countless allies to do so. Liu Kang states that he would bring them back in his own New Era, but Shang Tsung laughs at him: Liu Kang may be a god, but Shang Tsung has the flow of time at his beck and call.
In the end, destiny can favor only one...
In the White Lotus temple, a monk is looking over a jade dragon statue when he is approached by Lord Liu Kang, who tells this humble monk — the first, and later "Great" Kung Lao — that he must train and prepare...
Some time after, Raiden and Fujin, now thralls of the god Shang Tsung, report that Earthrealm, Outworld, and the Netherrealm have been conquered. Chaosrealm and Orderrealm are next.
With a smug chuckle and sly grin, Shang Tsung declares:
"It has begun."