The Deadly Alliance was a partnership formed between the demonic sorcerers Quan Chi and Shang Tsung. Together, the two villains enacted a plot to conquer all reality by pre-emptively destroying their greatest enemies and taking control of an ancient undead army. This partnership takes place in the video game Mortal Kombat: Deadly Alliance.
Many years following the defeat of Shinnok, Quan Chi - in possession of Shinnok's amulet - flees from his former servant Scorpion and finds a portal that allows him to escape from the Netherrealm. The sorcerer finds himself emerging in an ancient tomb in Outworld, a tomb that holds the remains of Outworld's former ruler, the Dragon King Onaga. Also contained within the tomb are hundreds of mummified soldiers which served as the Dragon King's army in ancient times. The soldiers were said to be invincible, but when the Dragon King was assassinated, they committed mass suicide and their mummified bodies were buried with him. According to the runestones within the tomb, the Dragon King's soldiers could be revived by transplanting the souls of slain warriors. Thus, Quan Chi sought out the assistance of a sorcerer well-versed in the art of soul manipulation: Shang Tsung.
Quan Chi met with Shang Tsung and told him of the discovery he had made. Tsung was intrigued by Quan Chi's plot and the two sorcerers reached an agreement. But before they could carry out their scheme, they would need to take pre-emptive action against those that posed the greatest threat to their plan. Firstly, the two approached Shao Kahn, emperor of Outworld, feigning allegiance to him as they met with him in his throne room. They then launched a swift attack against the emperor and appeared to have killed him. (It would later be revealed that the Shao Kahn the sorcerers had killed was actually a clone.)
With Shao Kahn eliminated, the Deadly Alliance then travelled to Earthrealm by way of a mystical portal known only to sorcerers and deities. There, they would confront Earth's mightiest warrior and champion of Mortal Kombat: Liu Kang. Shang Tsung had long desired revenge against Kang for past defeats and with Quan Chi's assistance he would at last achieve this goal. Disguising himself as Kung Lao, Tsung infiltrated the Wu Shi Academy where he found Liu Kang practising his kata. With his enemy in sight, Tsung dropped his façade and attacked. Liu Kang seemed to have the advantage during the fight, but he was then struck down from afar by Quan Chi who had cast a magical attack. With his rival's guard down, Shang Tsung moved in for the kill and snapped Liu Kang's neck. Earthrealm's champion was dead and Shang Tsung consumed his soul.
The Deadly Alliance then returned to Outworld where they went about rallying the remnants of Shao Kahn's army to their cause. With Kano and the Tarkatan hordes under their command, they invaded the village of Sun Do, enslaving its people and forcing them to build a grand palace for Shang Tsung. The palace would house a Soulnado, a portal to the Heavens that would allow Shang Tsung to access an unlimited number of souls, increasing his power exponentially. In the meantime, the Deadly Alliance hosted a fighting tournament in Sun Do, drawing warriors from across Outworld. Those who fell in battle would have their souls transplanted into the mummified soldiers of the Dragon King's army.
In the wake of Liu Kang's murder and Quan Chi's tapping of the Heavens, the thunder god Raiden relinquished his status as an Elder God and gathered the chosen warriors of Earthrealm in order to strike back against the Deadly Alliance. Travelling to Outworld, the heroes engaged the Tarkatan hordes in battle. Unfortunately, they ultimately failed to stop the Deadly Alliance from completing the resurrection of the Dragon King's army and most of the Earthrealm warriors were killed in the battle. Only Raiden himself remained to face Shang Tsung and Quan Chi, but the combined might of both sorcerers was too much for him and he was defeated also.
Both sorcerers had little time to relish in their victory and, unfortunately, quickly turned on each other. After a brief and vicious fight, Quan Chi stood victorious. He then turned his attention to a tall, massive intruder: Onaga, the Dragon King, who had returned from beyond death. It became obvious soon that Quan Chi could not stop the Dragon King. Even when Shang Tsung and Raiden regained consciousness and joined the fight against their common foe, Onaga was unstoppable. In a last ditch effort, Raiden released his godly essence in a terrible explosion which destroyed the palace, the Soulnado, the Deadly Alliance and Onaga's army, but not Onaga himself, who had now gained control of the Amulet of Shinnok. This marked the end of the Deadly Alliance.