The ninja returns unmasked. He was betrayed by his own ninja clan- the Lin Kuei. He broke sacred codes of honor by leaving the clan and is marked for death. But unlike the ninja of old his pursuers come as machines. He must not only defend against the Outworld menace but must also elude his soulless assassins.
In vicious battle Sub-Zero faces Cyrax and Sektor: but not alone. He finds his third Lin Kuei assassin- the elusive Smoke. Before automation Smoke and Sub-Zero were allies. Sub-Zero helps Smoke recall his past and gains him as an ally once again. Sub-Zero defeats his cyborg assassins with the help of Smoke and finds it takes all his own inner strengths to defeat Kahn and his Outworld minions. The former ninja once again disappears into the shadows. His legacy known only by a select few.