Shao Kahn first appeared in Mortal Kombat II as the final boss. A role he also served in Mortal Kombat 3. He is the main antagonist in the Mortal Kombat series.

The immortal Shao Kahn embodies evil in many forms. He is known for his godlike strength, extreme callousness, brutality and his fondness of personal executions. Shao Kahn also possesses great intelligence and knowledge of black magic. Much like Shang Tsung, he has the power to consume other souls. His greatest strength is probably his ability to relentlessly work towards his goals, and his skill at planning military attacks. However, his arrogance and overconfidence, has led to his failure in conquering Earthrealm. Shao Kahn originally served as an adviser to Onaga the Dragon King. Onaga's Empire had become the most powerful in the realms and so he began searching for a way to become immortal. Before Onaga could accomplish this goal, Shao Kahn poisoned him and stole his kingdom. He continued to add lesser realms to Outworld, either through direct conquest or through Mortal Kombat.

The greatest of all Shao Kahn's military victories was the merging of Edenia with Outworld. After his warriors had won in Mortal Kombat, Kahn invaded the realm. On the battlefield, Kahn killed King Jerrod, and took Queen Sindel as his wife, raising her daughter, Princess Kitana, as his own. He had the young princess trained as his personal guard and as an assassin. Sindel took her own life in an attempt to escape subservience to the Emperor. Unwilling to be denied, Shao Kahn held her soul in Outworld, stopping her transition to the afterlife.

Many years later, Kahn chose to conquer Earthrealm. He sent his best sorcerer, Shang Tsung and Goro to Earthrealm to prepare it for an invasion. Prince Goro defeated the Great Kung Lao and started a winning streak that would last for 500 years. During the tenth Mortal Kombat both Goro and Shang Tsung were defeated by Liu Kang. Shang Tsung begged Shao Kahn for his life, and came up with a plan to lure Earth's chosen warriors to Outworld for a second tournament. Shao Kahn spared Tsung's life and restored his youth. Once Earthrealm's champions were killed, nothing could stand in Kahn's way. With the captured Kano and Sonya Blade as bait, and enraging Liu Kang by sending Baraka and his troops to destroy the Shaolin temples, they confidently waited for the Earth warriors to fall into the trap. Despite Kahn's vast power he was defeated by Liu Kang. Unwilling to accept defeat, Kahn called his armies to destroy the Earthrealm warriors. They fled back to Earthrealm, barely escaping Kahn's wrath.

Shao Kahn was enraged by his defeat, and came up with another plan to conquer Earthrealm. He had Shang Tsung resurrect Queen Sindel in Earthrealm, and Kahn would be able to cross the border to claim her. Once he invaded Earthrealm, he began to merge it with his own realm of Outworld. Nearly every living being in Earthrealm had their souls ripped from their bodies by Kahn, claiming them as his own. Kahn sent extermination squads to hunt down and kill all remaining survivors. A handful of warriors escaped, and it would be up to them to try to stop Kahn, and return Earthrealm normal. Kahn was confronted by Kung Lao and Kahn cast a powerful spell on Kung Lao that nearly killed him. Liu Kang once again defeated Kahn. Worn down from the battle, Kahn recalled his squads and retreated back to Outworld. This stopped the merger with Outworld, and restored Earthrealm to its original status. To make matters worse for Kahn, many of his loyal soldiers had abandoned him, and Kitana had succeeded in turning Sindel to her side, restoring Edenia as an independent realm.

The emperor was now greatly weakened, and would be so for several years, remaining inactive during Shinnok's war against the gods. The Edenians had made peace and military treaties with the Shokan, which Kahn had always relied on, and were ready to attack Outworld a few years later. It was only through his new commander Kano's ingenuity, and the stealth of his unreliable assassin Noob Saibot was Shao Kahn able to save the day and force the Edenian army into a draw. Soon afterward, the sorcerers Quan Chi and Shang Tsung entered his throne room, and swore false allegiance to the emperor. Quan Chi and Shang Tsung caught Shao Kahn off guard and seemingly killed him. However, Kahn did not die; it was a clone that Quan Chi and Shang Tsung killed. The real Kahn appeared to the wounded Goro and, using what little power he had left, revived him, thus gaining Goro and the Shokan as allies once again.

Later on, he would form an uneasy alliance with Quan Chi, Shang Tsung, and Onaga in hopes of defeating Blaze and seizing his god-like powers. In his ending, Shao Kahn makes his way to the top of Argus' Pyramid for the final confrontation with Blaze. Shao Kahn proved to be too powerful for Blaze and easily defeated him. Shao Kahn's armies destroyed what was left of his enemies, and with the power Shao Kahn received from defeating Blaze, he merges all the realms with Outworld. With his main goal completed and having complete control over all the realms, Shao Kahn grew mad with boredom, as he had nothing else left to conquer.