i wrote this in another thread but i thought i'd add it to this active one too ...
My prediction on the boss/story line
The story is going to take the audience to Outworld and it is going to play out like Game of Thrones with a chaotic race to the throne of Outworld to sit as the emperor, with alliances and back-stabbings along the way. So i believe the main boss in MKX will have Outworld leadership as there motivation.
Mileena Boss Theory - Mileena is the rightful heir to Shao Kahn's thone as Outworld Emperor.
Reiko Boss Theory - The general of Shao Kahns army that always aspired/dreamt to one day be Emperor. Mileena wages war on Kotal Kahn to reclaim what is rightfully hers, being Shao Kahns only heir. Reiko gains Mileena's trust, helps her by leading her forces into battle only to betray her and take the throne for himself amongst all the chaos.
Reptile Boss theory - With Kotal Kahn "wanting to restore it" along with the aid of D'vorah & Ferra/Torr after the defeat of Shao Kahn. Reptile having some interest in restoring Outworld where his race once flourished offers Kotal his services to aid the war against Mileena , be it as a spy for Kotal or even a double spy, only to betray him/Mileena and take the throne as emperor for himself.
Baraka Boss Theory - Much like my Reiko and Reptile theory but somewhat combined. Similar motives to Reptile wanting to claim the throne of Outworld for himself and his people, and does so by helping lead the forces against Kotals Kahns army only to betray Mileena and Reiko amongst all the chaos.
now that i have written this out i thinking that these are probably more likely to be their character endings :/
But my moneys on Reiko being the final boss. it makes the most sense to me and he's be the only "surprising return Character" that fits the story we know so far, imo.
To add - I think we're saving Outworld this time around, not so much Earthrealm, and the bigger picture to Mortal Kombat, being the amulet, Eldergods, all that jazz will be resolved early in the story. Shinnok will be seen to early continuing on where the last mortal kombat left, and have Raiden capturing Shinnok in the Amulet once again with the help of Johnny Cage and Sonya Blade. Then the story is going to take us 25 years into the future, through the eyes of the next generation, the new Special Forces and to Outworld where there's a war going on.