Liu Kang is new head boss after beating Raiden and becoming a God.
Shinnok has Raiden join him, thus we see the evil "black garb" wearing Raiden again, teamed with Quan Chi.
They make some shit happen in all the realms to truly piss off the Gods.
Liu Kang gets other Elder Gods to join in crusade against the realms to "start over" if you will through genocide of EVERYONE. (Kotal Khan looks to be second from the left.)
The realms say FUCK THAT and MORTAL KOMBAAAAAAAT X(10 for fuck sake) starts.
This is just my thoughts at the moment on how Liu can be the main boss.