Thousands of years ago, Shinnok existed as an Elder God. The Elder Gods are the true rulers of all realms. They watch as worlds are created and destroyed and govern the realms with untold eons of wisdom. Shinnok, however, gave in to greed and illusions of false power by the new realm of Earth. If he could have that realm to himself, he would have power unmatched. To accomplish his goal, he first would have to face the young god of thunder known as Raiden, who was appointed as Earth's guardian by the Elder Gods themselves. Their battle for the realm of Earth was fierce; causing the planet's near destruction and plunging it into centuries of darkness.

Raiden soon discovered that Shinnok entered the realm through the powers of a mystical amulet. It allowed Shinnok to enter the realm without challenge and keep the other Elder Gods from intervening. The amulet could only be created once, and Raiden stripped it from Shinnok's possession. With the aid of the true Elder gods, he banished the fallen god into a place known as the Netherealm. Raiden buried the amulet deep within the mountains of Siberia. He then created a massive temple within the mountain to house the amulet and appointed four guardians as the protectors of Shinnok's sacred amulet. Each guardian represents one of the four elements that make up the realm: wind, earth, water, and fire. As long as the amulet remained on Earth, Shinnok would be trapped and forced to remain dormant for the rest of eternity.

Over the millennia, the Netherealm has had many rulers. Most of them were forged within its fiery pits, eventually ripping their masters mercilessly from their thrones. One, however, came not from the bowels of the Netherealm, but from the heavens of reality. He was the fallen Elder God known as Shinnok. Upon entering the realm, Shinnok found himself immediately under attack by its then ruler Lucifer. He would exist tortured and tormented for thousands of years, until he met Quan Chi.

Quan Chi is a free roaming sorcerer. That means that he can travel the various planes of reality without detection from their gods. It also means that over the years he has obtained great power. Aware of Shinnok's dilemma, Quan Chi traveled to the Netherealm and made the fallen god an offer. He will free him from his confines and assist him in defeating Lucifer and his minions in exchange for power and the ability to rule at his side if and when he escapes the Netherealm entirely. Shinnok agreed, and the two waged a war in the Netherealm that lasted for centuries, but the ex-Elder God eventually won as he viciously slew his former master. Then he took his seat as the new ruler with supreme control of the dead realm. Shinnok, however, had nothing to rule. The realm was a desolate wasteland of fire and brimstone inhabited by grotesque demons. So, he decided to create a physical world, trying his best to emulate the realm he wanted so badly, Earth. He took the demons of his realm and transformed them into as human a form as possible. But unlike the Outworld, which became a wasteland after Shao Kahn sapped its energies, the Netherealm never was a living planet. It always will exist as a dead world. Its true form hidden by its ruler.

It was through the Mortal Kombat tournament that the Outworld's soul-stealing sorcerer Shang Tsung discovered the location of the sacred Map of Elements, which could bring him to the sacred amulet. After Goro, the reigning Outworld champion, defeated the first Kung Lao over 400 years ago, Shang Tsung sapped the human's soul. He retained his thoughts and memories, thus discovering the secrets of the sacred map, which has been hidden within the Shaolin Temple for centuries. These events enabled Shang Tsung to strike a bargain with Quan Chi.

In exchange for Shinnok's assistance in a plot to reincarnate the Outworld Emperor Shao Kahn's dead queen, Sindel, Shang Tsung would reveal to Quan Chi the location of the map that would lead to Shinnok's sacred amulet. However, Shang Tsung failed to inform Quan Chi of the elemental guards that protect the amulet. Their mere existence makes it impossible for Quan Chi to enter the temple where the amulet rests. But, if he could get a human to enter, the right human, one who could perhaps defeat the elements, then he could acheive his goal.

Although released five years after the first Mortal Kombat game, the storyline in Mortal Kombat Mythologies: Sub-Zero dates back furthest chronologically, even before the first game. This was done to further expand and retcon elements on the existing storyline, especially concerning Quan Chi, Sub-Zero, Scorpion, Shinnok, and the Lin Kuei.

One of the most lasting rivalries in the Mortal Kombat series has existed between Sub-Zero and Scorpion. They were enemies in the first Mortal Kombat tournament in 1992, and Mortal Kombat Mythologies: Sub-Zero further explains the hatred between these two characters.

The human Quan Chi sought after to find the amulet was Lin Kuei warrior Sub-Zero. Quan Chi hired Sub-Zero and the Lin Kuei to find the amulet, and Sub-Zero was sent to find the map leading to its location. He did not know that Quan Chi had hired a Japanese ninja from the rival Shirai Ryu clan, Hanzo Hasashi, for the same task in case Sub-Zero failed. Hasashi and Sub-Zero encountered each other, where Sub-Zero killed him in cold blood. After Sub-Zero delivered the map, Quan Chi made good on a promise to the Lin Kuei; the rival clan, the Shirai Ryu, was wiped out. Hanzo Hasashi, also known as Scorpion from the rival clan of the Shirai Ryu, is also hired by Quan Chi to steal the same map from the Shaolin temple. The unsuccessful thief's clan was to be wiped out as payment to the other clan, though each is unaware of the other's involvement. Scorpion is killed by Sub-Zero, and the Shirai Ryu are destroyed by Quan Chi. This results in Scorpion's everlasting hatred of Sub-Zero. Though his attempt to kill Sub-Zero is unsuccessful, it sets up his return in the first Mortal Kombat game.

After Sub-Zero retrieved the map, he is hired again for another mission. This time, he is to follow the directions on the map to a hidden Temple of the Elements, wherein an amulet (supposedly Quan Chi's) is kept. Defeating the four elemental god-guardians in the temple, Sub-Zero finds the amulet. Quan Chi takes the amulet, revealing that it is actually Shinnok's amulet, capable of freeing the fallen Elder God Shinnok– Quan Chi's master– from the Netherealm and allowing to take over all realms. Raiden, who had placed the amulet in the temple in the first place to protect it from the likes of Quan Chi, appears and tells Sub-Zero to rectify his mistake and retrieve the amulet. Sub-Zero reluctantly agrees and is transported to the Netherealm. There, he tracks down Quan Chi and Shinnok, and steals the amulet back from Shinnok before he can use it. He then escapes to Earth via Raiden's portal. It is later revealed that Quan Chi had never given the amulet to Shinnok; instead, he had crafted a fake and kept the original for himself. This is crucial to the events of Mortal Kombat: Deadly Alliance in the years to come.

Although the game had a rather interesting notion and storyline, it was not well received by both critics or gamers. The graphics, although fluid on their own right, were considered outdated; it came out a few months before the polygon-filled Mortal Kombat 4. The story was seen as very complicated and difficult to follow in comparison with the previous games. It also had a sluggish gameplay, inadequate for a platform game. It was Mortal Kombat's only attempt to create a platform game. The fighting that took place within the game was often difficult. Although this game is placed higher on the list that Mortal Kombat: Special Forces, it is still regarded as one of the least favorite games in the series.