Something that is a bit... disappointing? Is that Shao Kahn was defeated by... a formality. Raiden's plan to defeat him was to let him step on earthrealm, and as the "contract conditions" stated that he couldn't do that if he didn't win the right by mortal kombat tournament, then the elder gods would punish him.

But was Shao Kahn really that dumb? He knew the consequences of his actions as well as Raiden, I don't think he really charged forward to take the realm without any sort of backup plan.

This is a guy that got his position through cunning instead of force. This is the guy that didn't let meet the Deadly Alliance himself and instead let them kill a clone. Shao Kahn is intelligent, not just strong, and have backup plans.

So here is my theory, I think that Shao Kahn though that he was strong enough to avoid any punishment the elder gods could inflict on him and that's why he tries anyway, but as the conquest of earthrealm had been particularlly hard, instead of risking everything he got a backup plan.

Somehow, through sorcery, he (or someone) made a new body and put that body in hibernation so in case of Shao Kahn's body being destroyed, his consciousness would inmediately jump to this new body (been done before in sci fi stories).

I think the body was Kotal Kahn, and that it was stored in some kind of tropical jungle in Outworld, and this is why he looks aztek and why Ferra/Torr that with their dialogue could be lackeys, also look like comming from that kind of area.

While gaining strength in this new body, Shao Kahn adopts a new identity and makes the people on this area venere him as a god. His personallity also might change a bit both because of the new body (with new brain) and because of his past experiences traumatizing him, so he now focuses on striking back at the elder gods and is trying to make himself a god to defeat them.

This could be an interesting twist if happening at the same time than Shinnokh's try or even later while they're weak.

Some people believe he might be the son of Shao Kahn, but it doesn't make sense he's the son because we would've known about him (unless he's a bastard born in one of the conquered realms maybe?).

It's just some random idea but honestly I can't believe Shao Kahn was fool enough to put his feet on earthrealm knowing what could happen.