During the time of the Deadly Alliance Sub-Zero travelled to the Outworld with Raiden along with his disciples and his student Frost. Sub-Zero fought Quan Chi with his student Frost. In the heat of battle Quan Chi punched Sub-Zero in the face and put Sub-Zero out of comission. Frost fought Quan Chi and was badly beaten to the brink of death. Sub-Zero managed to repel Quan Chi and escaped with the wounded Frost.

Sub-Zero was unable to defeat the Deadly Alliance and returned to Earth. Sub-Zero prepared his clan for the worst but however the Deadly Alliance had collapsed due to Quan Chi who killed his partner in evil Shang Tsung. Quan Chi was ready to lead the Dragon King's army into the Earthrealm but then the Dragon King had returned and killed Quan Chi.

The Dragon King once again controled his army and he was an unstopable force. The Dragon King entered the Earth realm and killed many. The Dragon King's army made their way to the Lin Kuei Temple and killed many of the Lin Kuei ninjas. In a fierce battle the Lin Kuei had collapsed and was destroyed. All were killed exept for Sub-Zero.

The Earth was left in ruins and Sub-Zero was left in shame. Sub-Zero had many things he tried to accomplish but now they were shattered. Sub-Zero wandered the ruined Earth in search of the Thunder God also known as Raiden.

Little did Sub-Zero know he was being spied upon. The spy was his deceased older brother who had returned from the dead due to the unbalance of the realms. Sub-Zero confronted his older brother and was told that the Dragon King's power comes from an ancient relic that lies within the Outworld somewhere. Together the two brothers traveled through a portal to the Outworld to strip the Dragon King of his power and to restore peace in the realms.