- Mortal Kombat (2011): "Emperor Shao Kahn's lust for power is matched only by his ruthlessness. Millenia ago he overthrew Onaga as ruler of Outworld and has conquered many other realms since. Eventually, he turned his attention to Earthrealm. The Mortal Kombat tournament prevents him from taking the realm by force, but if Shao Kahn's champions win 10 consecutive tournaments, Earthrealm will be his. As long as his champions Shang Tsung and Prince Goro do not fail him, he will be victorious."
- Mortal Kombat 11: "Emperor of Outworld. For millennia, Shao Kahn dominated the realms, rapidly expanding his Empire by conquest. But when he set out to claim Earthrealm, he was blocked by the rules of Mortal Kombat. Deterred but determined, Shao Kahn demands absolute victory."
Though he shared the same past histories as his original timeline counterpart prior Mortal Kombat, Shao Kahn has additional connections with his former general Kotal, and Kronika, such as betraying the former to be experimented by Shang Tsung, and learned about the latter's existence whom he thought to be a myth at first.
As the timeline shifts, the first Mortal Kombat tournament is the focus. While Shao Kahn is not there, he is monitoring the tournament. When Shang Tsung is defeated by Liu Kang, an irate Shao Kahn prepares to kill Shang Tsung. However, Shang Tsung offers an alternate solution for Shao Kahn: holding a tournament in Outworld with new rules. Shao Kahn agrees and rejuvenates Shang Tsung.
During the second Mortal Kombat tournament, Shao Kahn is physically present. He also makes some of the matches instead of Shang Tsung. Shao Kahn becomes frustrated when after Sub-Zero defeats Scorpion, the Lin Kuei cyborgs appear in front of him. While he allows them to take Sub-Zero away for automation and is granted the Lin Kuei's loyalty and service, he demands that Kitana explain why Earthrealm warriors are able to brazenly appear before him, when he had earlier ordered her to kill them. Before she can explain, he dismisses her, which allows Raiden the opportunity to sway Kitana to the Earth warriors' side. When Kitana discovers the experiments in Shang Tsung's Flesh Pits, she defeats Shang Tsung and brings him to Shao Kahn. Contrary to Kitana's expectations, Shao Kahn compliments the sorcerer instead. He then reveals to Kitana that her whole life has been a lie, and orders her to be executed and replaced by Mileena. In the process, Kitana's best friend Jade overhears this and aligns with the Earth warriors to rescue Kitana and defeat Shao Kahn.
Near the end of the second tournament, Shao Kahn pairs Shang Tsung with Quan Chi to face Kung Lao. However, they fail to defeat Kung Lao. Shao Kahn then sends out Kintaro to fight Kung Lao, but Kintaro also fails. As the arrogant Shaolin Monk celebrates his victories, Shao Kahn breaks the rules of the tournament by snapping Kung Lao's neck without issuing a challenge to Mortal Kombat. While Raiden attempts to electrocute Shao Kahn, an enraged Liu Kang assaults Shao Kahn. Liu Kang proceeds to defeat Shao Kahn, and punches a hole through his chest, mortally wounding him.
Later in the throne room, Kahn's lieutenants argue over who should be the new ruler of Outworld. The argument is quickly ended when Shao Kahn appears before them alive. It is revealed that Quan Chi used his sorcery to heal Shao Kahn. Upon returning to the throne room, Kahn berates Shang Tsung, as now Outworld has been forced to give up its claim to Earthrealm forever. Quan Chi, however, offers Shao Kahn an alternative solution: A direct invasion of Earthrealm.
Quan Chi explains that Kahn's former queen Sindel realized that the Mortal Kombat tournaments provided Earthrealm no real protection against Outworld. Thus, she committed suicide to create a barrier that would prevent Shao Kahn from physically entering Earthrealm and merging it with Outworld. Quan Chi goes on to explain that this barrier could be nullified if he were to resurrect and corrupt Sindel. Shao Kahn agrees to this, and in exchange, grants Quan Chi the souls of any Earthrealm warriors who are killed. With Sindel resurrected, Shao Kahn had an open window to merge Earthrealm with Outworld. He starts the invasion of Earthrealm as a result.
When Motaro is brought back dead, having been killed by Raiden, he is enraged. Sindel, however, states that she will finish what Motaro has started. To ensure that Sindel does not fail, Shao Kahn drains the souls from Shang Tsung's body, killing him. He then transfers the souls into Sindel. During this time, Kabal attempts to attack Kahn, but is intercepted by Mileena and Noob Saibot. After Kabal defeats Mileena and Noob, Kahn orders Quan Chi to seal the portal to Earthrealm, but Kabal manages to escape just in time.
After Sindel kills most of the Earth warriors before being killed herself by Nightwolf's sacrifice, Quan Chi reveals to Raiden in the Netherrealm that all of the souls of the lost warriors were granted to him by Shao Kahn. It is also during this time that Raiden discovers who "He must win" truly is: Shao Kahn. If Shao Kahn is allowed to merge the realms as he intends, he will be breaking the rules of Mortal Kombat, and the Elder Gods will destroy him.
As Shao Kahn appears to merge the realms, Liu Kang attempts to stop him, despite Raiden's warnings. This leads to a huge fight between the two, and it finishes when Liu Kang loses it and attacks Raiden from the back; Raiden electrocutes Liu Kang in self-defense, which much to Raiden's horror, results in Liu Kang's apparent death. Sonya and Johnny Cage attempt to stop Shao Kahn, who quickly incapacitates them with ease.
After this, Raiden surrenders to Shao Kahn. Shao Kahn gleefully attacks Raiden and beats him mercilessly. However, just as Kahn prepares to finish Raiden, the Elder Gods intervene, giving Raiden their powers. Raiden and Shao Kahn face off, and Raiden finally defeats Shao Kahn. As the weakened Shao Kahn attempts to attack Raiden one final time, Raiden blasts all of the Elder Gods' power into Shao Kahn, and the Elder Gods take Shao Kahn away for punishment. Raiden, Sonya Blade, and Johnny Cage then leave to help rebuild the world.
In the end, Quan Chi is seen picking up what's left of Shao Kahn's helmet. He then speaks with the fallen Elder God Shinnok, who reveals that all of the events in the game were actually part of Shinnok's master plan to escape the Netherrealm and take control of both Earthrealm and Outworld. After his death, Shao Kahn's soul later resided in Ermac in the next game.
Shao Kahn is featured in several flashbacks throughout the comic. As revealed by Kotal Kahn, Shao Kahn invaded the realm of Osh-Tekk ages ago, slaughtering the warrior race alongside his champion, Goro. When the ruler of Osh-Tekk, Kotal K'etz, surrenders, Shao Kahn allows him to keep his realm's treasure, the Portal Stone, in recognition for the Osh-Tekk's obedience. Shao Kahn would then merge Osh-Tekk into Outworld.
Sometime later, Shao Kahn, joined by Goro and his general, Reiko, would invade the Arnyek Islands before the Kytinn's could mount a proper defense. While other Kytinns ran at the sight of the emperor, one did not, and Shao Kahn demanded to know why she did not, at first believing her to be the queen of her people. The Kytinn declared herself the Kahn's humble servant and knelt before him. Shao Kahn ultimately spared this Kytinn, D'Vorah, from her people's fate and allowed her to serve him.
During the events of Shang Tsung's final tournament in Earthrealm, Shao Kahn ordered Reptile to enter, believing the sorcerer to have his own agenda and demanded Reptile do whatever he must to ensure victory. When Reptile continued to suffer defeat after defeat, Shao Kahn ordered Kotal Kahn to execute the Saurian for his failures but Kotal Kahn instead requested to take command over Reptile. Despite Kahn's reservations, he allowed it.
Before his death, Shao Kahn had become impressed with his general Reiko's ruthlessness in conquering in his name and adopted him.
Though long dead, Shao Kahn's weapon, the Wrath Hammer, would be wielded by Kotal K'etz when he was tasked with hunting down the traitors Reiko and Mileena. Goro would reclaim the hammer from K'etz after killing him, and Reiko took the hammer with him to Shang Tsung's Island, where Ermac would give it to Kahn's heir, Mileena, the weapon used to kill Reiko in a single blow, though not permanently due to his soul being tied to the Blood Code at the time.
Mortal Kombat 11
When Kronika begins manipulating the present timeline in preparation to create a New Era, the past era collides with the present, and as this effect takes hold in Outworld, Shao Kahn returned, emerging from the sandstorms of time whipping through the koliseum alongside his enforcers, the similarly previously deceased Tarkatan chief Baraka, the blood mage Skarlet, and the Black Dragon mercenaries he had forged an alliance with, Kano and gunslinger Erron Black, along with several of his own soldiers, in the middle of an execution attempt on Shao Kahn's debt Kollector. Shao Kahn is initially confused by the unfamiliar sights now in the koliseum and is outraged when he hears his former general Koa'tal declare himself as a Kahn.
Shao Kahn at first believes it is a trick by the thunder god Raiden, who along with his champions, arrived in the present alongside the konqueror, but upon learning from Kotal that he and his heir Mileena are both long dead, Shao Kahn demands Kotal vacate his throne, and when the Osh-Tekk refuses, he summons his Wrath Hammer and engages in a brief but fierce duel with Kotal. Though Shao Kahn suffers a wound to his shoulder from Kotal's blade, his raw strength overpowers the usurper, giving him the upperhand for a brief moment before their battle is interrupted by the time displaced Liu Kang, which causes an all out brawl to erupt in the koliseum as those loyal to Shao Kahn battle those loyal to Kotal, with Raiden's champions joining with the Osh-Tekk's forces to stem the tide.
After Kotal survives against Shao Kahn's personal enforcers, the Osh-Tekk emperor resumes his battle with the konqueror and emerges victorious. Before Kotal can execute Shao Kahn and his loyalists, he is rescued by the timely arrival of the Kytinn D'Vorah, who whisks Shao Kahn and his followers to her Hives. There, Shao Kahn learns from D'Vorah of his death at Raiden's and the Elder Gods hands, as well as Mileena's to D'Vorah from the Kollector. Infuriated that his daughter was killed, Shao Kahn moves to attack D'Vorah when Kronika, the Keeper of Time arrives. Shao Kahn finally confirms that Kronika does exist in front of his eyes.
She offers Shao Kahn an even greater empire in the New Era she seeks to create if he could take his throne back and rally Outworld's armies back under his flag to protect Kronika as she prepares to erase time. Shao Kahn readily agrees, eager to retake his empire and make it greater than ever before and destroy Raiden. Shao Kahn then moves himself and his followers to the Tarkatan Kamp along the edges of the Wastelands of Outworld, where he readies the Tarkata horde for civil war and prepares to reclaim the throne.
When Kotal Kahn and the past Jade's infiltration of the Kamp fails, Shao Kahn finds the two just after Jade has defeated Kotal for attempting to execute innocent Tarkatans for crimes their future selves committed for siding with Mileena. Shao Kahn has both imprisoned, giving Jade to Skarlet so she may feast on her blood while preparing to take Kotal back to the koliseum for public execution as a symbol of his victory and reclamation of his throne. As he boasts to the bloodthirsty krowd that Outworld's true ruler had returned and that they shall become konquerors once again, the koliseum is besieged by the united forces of the Tarkatan and the Shokan, led by Baraka and Queen Sheeva, with Shao Kahn's own adopted daughter Kitana having successfully rallied them to her side. Though he expresses impression at her boldness, stating that if she had shown it before, he never would have needed Mileena. Kitana retorts that both her adopted father and twin were unholy monsters before engaging him in a fierce duel that is interrupted by the Kollector.
Infuriated as Kotal is freed from his binds by Jade, the two Kahns resume their duel, and this time, Shao Kahn emerges victorious, crippling the Osh-Tekk by breaking his spine over his shoulders. Kitana confronts her adopted father before he can kill Kotal, and Shao Kahn mockingly bemoans letting Kitana live after killing her father, Jerrod, sneering that he never wanted Jerrod's heir, only his wife. He the goes on to say that he kept Kitana alive only to make his new queen happy. Shao Kahn then battles Kitana and is defeated by his adopted daughter, who knocks him flat onto his back on the sand floor of the koliseum, after declaring that she would not inherit his cruelty, Kitana tears away the mask of his war helmet and slices his eyes with her fan blade, blinding the tyrant and defeating him once and for all, avenging her parents and her kingdom. What becomes of Shao Kahn after this is unknown due to Kronika's reversal of time and creation of the New Era.
- Mortal Kombat 11 (Non-Canonical): "I conquered history like I conquered realms – merging billions of potential timelines into a Singularity. The universe has been remade in my image and all is as it should be. The weak serve the strong. The strong compete for power, wealth, and my favor in Mortal Kombat. For centuries, the tournament's champion has gone undefeated. That champion...IS ME! Hail the Conqueror! Hail Shao Kahn!"