Following his brother's failure to assassinate Shang Tsung during the first tournament (and his eventual death therein at the hands of Scorpion), the young Lin Kuei warrior took up his brother's name and was sent to Outworld to complete the assignment after Mortal Kombat II was announced. He soon discovered Scorpion's foul vendetta against his brother. Scorpion, aghast upon learning of Sub-Zero's apparent survival, continued to hold a grudge against the new Sub-Zero, as he believed him to be the same man responsible for his death. However, his belief was dispelled when he witnessed Sub-Zero spare the life of a defeated opponent during the tournament. Scorpion then came to the realization that this new Sub-Zero was the younger brother of his murderer, and, unbeknownst to Sub-Zero, swore not to harm him. Though Sub-Zero's attempt to dispatch Shang Tsung was fruitless, he successfully assisted Liu Kang, Raiden, and their allies in Liu Kang's battle with Kahn

In the events leading up to Mortal Kombat 3, the Lin Kuei obtained technology that could vastly improve the effectiveness of their warriors, and they chose four of their number to undergo the procedure that would turn them into cyborg assassins: Sub-Zero, Smoke, Cyrax, and Sektor. Sub-Zero and Smoke refused to participate, and fled the clan, who declared them anathema. While Sub-Zero successfully managed to escape, Smoke was captured and subsequently turned into a cyborg. In leaving the clan, Sub-Zero had broken the Lin Kuei codes of honor. After Smoke's automation, the Lin Kuei programmed the three cyborg assassins to hunt and terminate Sub-Zero, who by this time had received a vision from Raiden and agreed to join the rebellion against a new threat.

The armies of Shao Kahn attacked Earthrealm, and Sub-Zero was among the few mortals whose souls were spared so they could fight Kahn and his extermination squads. These events also signaled the beginning of Sub-Zero's transition to a greater moral consciousness. Sub-Zero eventually encountered Smoke and convinced him that he still had a soul, which then overrode Smoke's Lin Kuei programming. With his new ally, Sub-Zero then defeated both Sektor and Cyrax, then reprogrammed the latter to (unsuccessfully) terminate Kahn. Smoke was less fortunate: he was captured by Kahn's troops and transported to Outworld as a curiosium.