Hanzo Hasashi, better known as the warrior Scorpion, is summoned to meet with the Shogun of Kumamoto Castle. While traveling, the fearless General of the Shirai Ryu clan encounters his mortal enemy, Sub-Zero. Scorpion realizes too late that this trap has led him away from his village and family, leaving them without means to defend themselves. He knows that he must defeat Sub-Zero and return to his village before it is too late.

Cyrax and Sektor are chosen to be the future of the Lin Kuei by the Grand Master, but Cyrax is less than enthusiastic about giving his life over to a cybernetic transformation that will erase his memories and turn him into the ultimate fighting machine. When he discovers that the cyborg he is fighting seems closely familiar, Sektor must keep Cyrax focused on destroying Hydro, and not himself or their future...