Well, since he was in UMK3, he technically was in MK3, he just didn't play a big role at all. They said he returned to earth when Kahn failed to seize the souls that occupied hell, and then they had him allying with Kahn briefly for some reason. Of course, in his ending, it says his allegiance to Kahn falters when he discovers that one of the chosen warriors is the Sub-Zero he had vowed to protect, so he turns against Kahn and defeats him. But then that's just another one of those damn "what if" endings.