The game will take place as a prequel to the events featured in the first three Mortal Kombat games. It starts as a simple mission. Sub-Zero must steal a sacred map from an ancient Shaolin temple, but soon delves into a much deeper journey. The map is known as the Map of Elements- and it shows the way to a temple long hidden from the eyes of mortal men. But, the real treasure is what's housed within the temple walls. An artifact that predates man's history on Earth… an artifact known as Shinnok's Amulet.

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 could have that realm to himself, he would have power unmatched. He first would Earth. If he 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 planets near destruction and plunging it into centuries of darkness. But, the thunder god eventually won as Shinnok's overconfidence proved to be his undoing.

Raiden 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 Rayden stripped it from Shinnok's possession. With the aid of the true Elder Gods, Rayden banished the fallen god into a place known as the Netherealm. Determined to keep the amulet from ever falling into the wrong hands, Rayden buried it deep within the mountains of China. He created a massive temple within the mountain to house the amulet and appointed four immortal guardians to keep watch. As long as the amulet remained on Earth, Shinnok would be trapped, forced to remain dormant for the rest of eternity.