Earthrealm is pretty much screwed with most of the more powerful champions part of the undead, so I'd rather see the minions and the surviving heroes form an uneasy alliance

I'd definitely feel that Mileena and Baraka will return in the sequel along with Reptile and Ermac. They all have so much potential character development to build up. And Shang Tsung...maybe a surprising twist will happen? He is a sorcerer after all...

Ermac: he can fight for the good guys. he wound up joining them in deception due to Kenshi freeing him or whatever he did, so why not have that happen earlier.

Rain: he might join shinnok if he promises Rain he can rule edenia for his services.

Reptile: he should join the fight with the good guys. Give him a little change up, since Shao Kahn is gone, maybe Raiden could take this opportunity and try recruiting him somehow. Maybe he can tell reptile he'll put word in to the elder gods to try to ressurect his race/realm Reptile helps to fight against evil? idk

Mieena: i have a feeling she will work with shinnok because shinnok will promise her the same thing he promised Rain. Can start a side beef between mileena and rain.

Baraka: he can join Shinnoks side if Shinnok promises him the rule of outworld. I feel Baraka should be the type of character to seek power, make him a bad ass bad guy. try to give him more of a personality.

Skarlet: extremely loyal to shao kahn, but she should fight with the good guys, they need more allies so work out an alliance with her somehow.

Cyrax: maybe he can be stuck in the desert like in the original timeline, but this time sonya finds him and does what jax did to cyber sub zero and make him an ally. Later on joing the special forces.

Sektor: i don't really see fit for him here. maybe he can be on search for cyrax then realizes cyrax has joined the other side and he decides to join shinnok to eliminate cyrax for his betrayal.

just throwing out some idea's

I could see Skarlet being an unintentional ally. From what we know of her so far, she barely seems sentient at all. She's basically Shao Kahn's own Terminator. Her helping the heroes fight Shinnok would be purely coincidental. She might even attack them, and other minions of Shao Kahn, because her master isn't there to keep her in check (or should I say in chains) and to tell her who she should attack and who she shouldn't. If Quan Chi's MK9 ending partially happened and Kahn's soul is now under his control, he could command Skarlet through him.

I don't really consider the cyborgs Shao Kahn's official lackeys. Their alliance with him was most certainly a case of lumping baddies together, though they did offer a satisfying explanation as to why they joined him, admittdely. But anyway, in the cyborgs' case, I was thinking that both their endings should partially happen, as they don't contradict MK9's story mode at all.

Speaking of Shao Kahn's minions, and endings that could partially happen, let's not forget Sheeva. I'd love to see her become a definite ally of earth, like Kitana in the old timeline.

If Liu Kang returns, so should Goro, to try and reclaim his title as the MK champion like in the old timeline. After encountering and fighting Liu Kang, Goro would put aside his grudge to help fight Shinnok. If Liu Kang's dead, and his soul in Quan Chi's possession, Goro could try to liberate him just so he could have his rematch. Maybe there could be tension between Goro and Sheeva, with Goro viewing Sheeva as a deserter who left her world behind to immigrate to Earth, and gain her own position of power.

Finally, for now, Kintaro. Still a vague character after all these years. It's a little harder to guess whether he'd join Shinnok or fight him (and I'm not sure his appearance in MKA's konquest mode really counts). Can you imagine him fighting along the heroes? Maybe he could get a chapter of his own, where he fights nothing but other boss-level foes (like the giant cyborgs from MKM). he could be inserted into that conflict between Sheeva and Goro that I mentioned above, where he takes a stance against one of both of the other two Shokans. All three of them against each other.

I'd rather have Skarlet be neutral rather than become randomly good because Kahn is dead.

I also hope that Reptile is not going to go for the whole, "Maybe Shinnok can resurrect my race so I'll stick with him," if he still becomes evil rather than a neutral character as well. I hope he becomes neutral.

As of right now, I don't know what Ermac should become. I'd like to see his arcade ending become canon, but then again, I don't know. I'm a little if-y about this character.

I do hope for Reptile to become good.

As for Ermac, hope its King Jerrod taking over permanently.

As for Skarlet... either evil or neutral. That's a tough decision.

Rain can also become a part of Shinnok's forces.

Does anyone think Jerrod will ever be brought back into the story somehow? We know no one ever really dies in MK, so...

Um guys.
Skarlet is a weapon. The only thing she knows is how to fight and kill. Hell she can't even speak. She will be hostile towards everyone,wether evil or not it doesn't make difference.
Why do you think Shao Kahn keeps her chained up in the first place. He uses her only as a last resort, since he knows that Skarlet is uncontrollable and will attack everyone, like a angry bull let lose.

About the others Reptile and Ermac should join the good guys, Mileena and Baraka should be independent and Rain should join Shinook.
And they better bring the dead heroes back. At least Sub zero and Kitana