So what i've gathered from Kotal Kahn is that he has Outworld's best interest in mind but in the manner he is doing it conflicts with the heroes. We can clearly see he uses blood magic & actually rips people's hearts out & drinks the blood. Not something a hero would do.

If I had to compare him to someone I'd say he seems to be a lot like Sinestro. He wants the best for his people but still craves power. In his mind he is the hero.

More or less my thoughts. I would say he is the protector of Outworld, like Raiden is of Earthrealm. He may have been imprisoned by Shao Kahn, and he got free with his death.
That said this requires an explanation of his whereabouts in the first timeline.