Here is my theory of mine for the next MK game
OK here is my theory on the "twist" ending with Shinnok. It starts with MK: Mythologies in the original timeline, Quan Chi deliberately withholds Shinnok's amulet keeping it for himself and giving Shinnok a perfect but powerless replica. My theory is that Shinnok was aware of Quan Chi's deception from the start and instead of confronting him about it and risking losing a powerful follower or having Quan Chi stash the amulet somewhere he simply let Quan Chi think he was fooled.
Then he made a "twin" of himself that launched the Netherrealm offensive of MK 4 with Quan Chi that was ultimately defeated by the forces of light. My theory was that for Shinnok this was a carefully planned feint; everyone thought his double was the real elder god and when he was defeated and sent back to the Neatherrealm people stopped tracking his movements, just what Shinnok wanted! (Seriously, do you think an elder god, someone with power in excess of Raiden's could be defeated so easily?) With eyes off of him he was free to keep an eye on Quan Chi and the amulet as well as other parties of interest such as Raiden and Liu Kang. The arrival of Onaga and the Kamidogu on the scene provided an interesting twist; you see he knew about the coming Armageddon, he was friends with Argus and Delia as evidenced by Taven calling him "Lord Shinnok" and treating him reverently. Through this association he must have heard about Armageddon from them prior to his banishment. Realizing he could not rule the realms if they were all destroyed Shinnok began biding his time in the Netherrealm waiting to see how things would turn out. In the midst of the battle with Onaga the Pyramid of Argus appeared with Blaze atop and Shinnok knew it was again time to send a twin into battle.
The defeat of his twin on the battlefield was irrelevant, it was only a distraction; (and if one remembers Shinnok's Armageddon ending the power of Blaze makes his twin equal to the original Shinnok meaning a Shinnok vs Shinnok battle.) he is perfectly aware of Raiden's defeat and Shao Khan's victory. The timeline shift means nothing to an elder god, he is fully aware of the previous timeline, Quan Chi's betrayal and everything that happened up until Raiden's death.
In the alternate timeline Quan Chi and Shinnok carefully plan to give aid to Shao Khan in order to build up his confidence. The emperor of course is blissfully unaware that the elder gods will punish him for merging the realms without MK. The outcome with Khan is no surprise to the two as they can be seen conversing at the end of the game. The real surprise is for Quan Chi, he is unaware that Shinnok knows of his betrayal; in fact I believe that during the contents of the game (off-screen of course) Shinnok switched the real amulet that Quan Chi had in his possession with the counterfeit one! Meaning that Shinnok now has the real amulet and Quan Chi the fake with Shinnok being the only one that actually knows this!
So the next game in the series will be the "real" MK 4 where the full unrestrained power of an elder god is what is threatening Earth realm! I wonder how Raiden will deal with this, especially since Johnny Cage and Sonya Blade are the only other kombatants left for Earth realm.