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As humans, Elder Sub-Zero kills Scorpion. He once again defeats Scorpion, in the Netherrealm where Scorpions' powers are even enhanced. This happens in MK Mythologies. Scorpion then kills Sub-Zero in MK1 and in this reboot (Probably in the Netherrealm as in this game).
After this, in the original timeline they do not see each other ever again. Scorpion defeats younger Sub-Zero (MK4), and so does Noob Saibot (MK Armageddon). Scorpion gets beat up by Drahmin and Moloch whenever he attacks Quan Chi. Noob Saibot kills Goro (Originally), albeit Goro was exhausted from battle. Scorpion however is selected by the Elder Gods as their defender of the realms, while Noob Saibot is trying to build an army of cyber demons. I'd say it's a tie.