Story Mode
In the aftermath of the Battle of Armageddon, all kombatants have been killed save for two: Raiden and Shao Kahn, the latter of whom defeated Blaze and obtained godlike power. Raiden is badly beaten and near death when he enacts a final, desperate plan to prevent the destruction of all known existence that would occur with Shao Kahn's victory: using the pieces of his cracked amulet and the last of his power, he sends a series of visions back in time to his younger self, along with the message "He must win..."With the commencement of the Mortal Kombat tournament that would determine Earthrealm's fate, Johnny Cage, an actor from Hollywood, is called to take part in the first fights of the tournament. Cage manages to defeat the Zaterran ninja Reptile and the Tarkatan warrior Baraka, but when instructed by the host Shang Tsung to finish them, Cage balks. He is congratulated by Raiden and his charge, the Shaolin monk Liu Kang, who both warn him that Earthrealm is in peril. Cage, however, doesn't take the warning seriously and goes to pursue a woman he became smitten with: Sonya Blade.
Sonya, however, is unreceptive to Johnny's advances, and attacks him in frustration, forcing him to fend her off in self-defense. When they are subsequently ambushed by the notorious criminal Kano, however, Johnny Cage defeats him, earning him Sonya's begrudging respect as she informs him that she came to the Mortal Kombat tournament in search of her superior officer, Jackson "Jax" Briggs, and sets off in search of him.
After healing Jax's wounds, Raiden explains to the Earthrealm warriors that he is receiving messages from the future, one that paints a grim fate for Earthrealm, if not all of existence. For the time being, however, he believes the best course of action is to allow events to play themselves out...
Afterwards, Scorpion encounters two Lin Kuei assassins, Cyrax and Sektor, who taunt him over his clan's death and challenge him. After defeating them, he confronts Sub-Zero and drags him to the Netherrealm. Scorpion emerges victorious, but decides to spare Sub-Zero as per Raiden's wishes. Quan Chi, a sorcerer who came to the tournament with Scorpion, questions his decision and shows him visions of the Lin Kuei's extermination of the Shirai Ryu, with Sub-Zero being personally responsible for the deaths of his wife and child. In spite of Sub-Zero's pleas of innocence, Scorpion's rage gets the better of him: when he returns from the Netherrealm, all that remains of Sub-Zero is a charred skull and spine.
Cyrax, one of Sub-Zero's allies, vows revenge against Scorpion. Raiden, however, chastises him for his clan's perchance for "ruinous decisions", including the Cyber Initiative: a project to convert all Lin Kuei into cyborgs, and he questions his allegiance with Shang Tsung...
Cyrax emerges victorious over Cage, but refuses to kill him. Sektor confronts him over his rebellious actions against the Lin Kuei, but Cyrax defeats him and declares that he is through with the Lin Kuei.
Later, Liu Kang is ambushed by Kitana. Having taken a shine to her, Liu Kang spares her after defeating her, even though she begs him to finish her: he tells her that their fight never happened, and that he'd like to meet her again, albeit under different circumstances.
After fighting and defeating both Scorpion and Quan Chi, Liu Kang goes up against the current Mortal Kombat champion, Goro. After besting the Shokan prince, Liu Kang engages in one final fight with Shang Tsung and defeats him. With Outworld's victory streak broken before they could secure the final victory they needed to invade, Earthrealm's safety is secure.
Everything is happening as Raiden foresaw in his visions. Yet, more cracks begin to form in his amulet...
Meanwhile, Shang Tsung is threatened with execution by Shao Kahn for his failure. Shang Tsung, pleading for a second chance, proposes a new plan, one that may see victory for the Outworld emperor yet...
Raiden, deciding that events at this tournament must play out differently than in his visions, brings Jax and Johnny Cage with him to Outworld, where the final tournament will be held. Jax defeats Baraka, but the tournament is postponed when Shang Tsung is forced to attend to other matters.
Raiden receives a vision of Sonya about to be executed, and teleports himself, Cage, and Jax to Shao Kahn's armory in search of her. After getting into a fight with Johnny Cage when he insists Jax was more than a "superior officer" to Sonya, he is confronted by Jade, whom he defeats.
Discovering Sheeva and several guards holding Sonya prisoner at the Dead Pool, Jax fights her while Raiden and Cage fight the guards, defeating her and rescuing Sonya.
Sonya's wrist device then picks up two foreign signatures having arrived in Outworld, and the group decides to split up to locate them in hopes of finding the one who must defeat Shao Kahn, with Raiden and Johnny Cage heading for one, and Sonya and Jax to the other...
The two split up, and Smoke is attacked by Kitana. After defeating her, he finds Kano and Shang Tsung in the Living Forest, making a transaction: Kano offers high-tech weapons to Shang Tsung and the forces of Outworld in exchange for a nominal fee. When Smoke demands to know Sub-Zero's location, Kano steps in to fight him, but is defeated. He then fights both Reptile and Shang Tsung (who adopts Sub-Zero's form). After defeating them, he is ambushed by Sektor, who has now been converted into a cyborg, as per the Cyber Initiative. Sektor demands Smoke return to be Cyberized, and although Smoke manages to fend him off, he is subdued by several Cyber Lin Kuei. Fortunately, Smoke is rescued by Raiden, who had received a grim vision of him being forcibly Cyberized. Grateful towards the Thunder God, Smoke decides to ally himself with him as they set off to find Sub-Zero, whom Smoke fears is also in danger...
When Sub-Zero demands to fight Scorpion, Shao Kahn makes him fight Reptile instead. After defeating the Zaterran, Shao Kahn agrees to oblige Sub-Zero's demands and Quan Chi summons Scorpion. In the ensuing fight, Sub-Zero emerges victorious, but before he can finish Scorpion, he is subdued by the Cyber Lin Kuei, and Cyrax and Sektor offer their services to Shao Kahn in exchange for Sub-Zero.
Raiden and Smoke arrive at the coliseum, but Raiden forbids Smoke from interfering, fearing that letting Smoke be captured and Cyberized would lead to calamity: Sub-Zero, thus, is lost to the Lin Kuei.
Her curiosity piqued, Kitana heads to the Flesh Pits. She is confronted by Jade in the Living Forest, who begs her to turn back, but Kitana defeats her and continues into the Flesh Pits. There, she finds tubes belonging to Shang Tsung that house several clones of her, albeit infused with Tarkatan blood: the clones look exactly like her, except for their amber snake-like eyes and their large mouths lined with razor-sharp teeth.
One such clone, having awakened, attacks her, but Kitana defeats it. She is then confronted by Shang Tsung, whom she subdues and places before Shao Kahn to face judgment. To her horror and outrage, however, Shang Tsung is praised for his creation, dubbed "Mileena". In addition, Shao Kahn reveals to her that he is not her father: she was merely adopted by him after Outworld's konquest of her home realm of Edenia, where she was the daughter of its king. Shao Kahn orders Kitana executed at the Coliseum.
Both Shaolin go to the Coliseum as things look grim for Earthrealm, with Johnny Cage and Smoke bested, and Sonya and an injured Jax having already fled. When Shao Kahn demands a new opponent from Raiden, the Thunder God elects Liu Kang. Liu Kang, however, doesn't believe he is the one destined to win, and goes to save Kitana. Raiden then selects Kung Lao to fight in the tournament. Lao goes up against the Deadly Alliance of Shang Tsung and Quan Chi, as well as Outworld's new champion, the Shokan Kintaro. He emerges victorious, but is suddenly killed when Shao Kahn snaps his neck while he celebrates his victory.
Enraged, Liu Kang challenges Shao Kahn to Mortal Kombat. He manages to land a devastating blow upon Shao Kahn, driving his fist through his torso, killing the tyrant, winning the tournament and forevermore securing Earthrealm's future...
...or so he thinks. Even with Shao Kahn's defeat, more cracks form on Raiden's amulet.
To make matters worse, Shao Kahn survived his injury with the aid of Quan Chi, and is absolutely livid about Shang Tsung's gambit backfiring, causing him to lose any right to merge Earthrealm with Outworld. Quan Chi, however, proposes a new plan: supersede the Elder Gods' authority by invading Earthrealm directly. The plan seems impossible at first, since Sindel, the queen of Edenia and Shao Kahn's bride following the realm's konquest, placed a protective ward on the realm when she killed herself to spite Shao Kahn. With Quan Chi's necromancy, however, he could not only undo the protection by resurrecting her, but ensure she remains loyal to Shao Kahn. The plan succeeds, and Earthrealm's invasion begins not long after...
Shao Kahn is seen mourning the death of Motaro, whom Raiden slew to prevent Johnny Cage's demise. He then drains Shang Tsung of his souls, killing him in the process, and transfers them to Sindel, increasing her power severalfold.
Kabal approaches Shang Tsung, but is attacked by Mileena and Noob. He defeats them and escapes through a portal to Earthrealm, but is then attacked by a Cyberized Sub-Zero. After defeating him and fending off Sheeva, who mistakes him for one of the Cyber Lin Kuei, he is rescued by Raiden, who brings him and an unconscious Sub-Zero to a church where the Earthrealm warriors are being sheltered.
Upon returning to Outworld, however, Sektor realizes that Sub-Zero had been reprogrammed. He takes him back to Earthrealm and attempts to undo Jax's modifications, but Sub-Zero subdues him and hacks into his neural network, learning that Outworld forces have gathered several Earthrealm military personnel at a church. He goes there and freezes Kano before defeating Kintaro and Goro, and then Ermac, saving the soldiers they had gathered in the process. He learns from them that other soldiers had been taken to a nearby cemetery.
There, he finds Quan Chi preparing to create a Soulnado that would absorb all souls in Earthrealm. He is confronted by his undead elder brother, Noob, but manages to defeat him. Unfortunately, Quan Chi completes the spell and generates the Soulnado.
While Raiden and Liu Kang are away, the Earthrealm warriors are ambushed by Sindel and the Lin Kuei. Nightwolf defeats Cyrax and then Sektor, but Sindel manages to kill most of the Earthrealm warriors, save for Nightwolf, Johnny Cage, Sonya Blade, and a gravely-injured Kitana.
By the time Raiden and Liu Kang return after learning that Shao Kahn's actions did not violate any rules with his invasion of Earthrealm, Nightwolf is left with no option than to sacrifice himself to destroy Sindel. As Kitana dies in Liu Kang's arms, Raiden, now desperate, decides that he has no choice but to form an alliance with Quan Chi. Liu Kang, shocked at this decision and now believing Raiden to have gone mad, refuses to accompany him...
Raiden returns to Earthrealm to tell Liu Kang that Shao Kahn must be allowed to merge Outworld with Earthrealm. This proves to be the final straw for Liu Kang, who tries to attack Shao Kahn before he can enter Earthrealm. Raiden stops him, and the two come to blows. Raiden uses an electrical barrier to fend off a fiery punch from Liu Kang, but accidentally sics his flames back on him, mortally burning him. Liu Kang curses Raiden before dying, just as Shao Kahn emerges in Earthrealm.
Johnny Cage and Sonya Blade try to fight Shao Kahn, but are rebuffed with ease. Raiden, realizing he can't win, leaves himself to Shao Kahn's mercy. After pummeling him in a similar manner to the grim future Raiden foresaw, Shao Kahn prepares to kill him. However, the Elder Gods finally intervene, acting through Raiden's body and fighting Shao Kahn.
Shao Kahn is defeated and utterly destroyed by the Elder Gods. Earthrealm is saved, but the cost was greater than anyone could've imagined. As Raiden leaves with Cage and Sonya to help in rebuilding Earthrealm, Quan Chi appears: throughout all of these events, he had been acting as an agent of the fallen Elder God Shinnok. With Earthrealm and Outworld in a weakened state following their war, the Netherrealm is in a prime position to conquer both once Shinnok is freed from his prison...
