What do you think of, rather than having one Ultimate evil being, or group, about having each individual character have their own individual strugles, with a few threats, such as attacks by the remaining tarkatans, Shao Kahn and Goro's Shokan army, and individual rivalries. In MK:D, i noticed most characters never really participated in the final fight, but had other events as more important points to their story.

For example:
Assuming Sub-Zero and Kenshi's storys are true, the duo could continue onwards to a portal back to Earthrealm. Apon arriving at Earthrealm, and traveling back to the new Lin Kuei sight, the Grandmaster could be attacked by renegade Lin Kuei, refusing to accept the recent changes to the clan. A faction against him has grown in his abscence. Sub-Zero, although outnumbered, with the help of Kenshi, managed to fight off this threat and return to the Lin Kuei's new sight, wounded. Apon arriving, Sub-Zero would realise that only a small portion of the original Lin Kuei would remain, the rest returning to their former lands, vowing to destroy the new Lin Kuei. Sub-Zeroes story could then revolve around rebuilding his followers, similar to the Black Dragons, and then taking on the other Lin Kuei. He would travel with Kenshi, a new Lin Kuei member, towards the former home of the Lin Kuei.

So instead of fighting a bunch of random enemies and then facing off against the main boss like in previous games, Sub-Zero would fight opponents relevant to his story. So he may fight a few of the Lin Kuei warriors who were sent to defeat him in the beginning, that survived the ordeal. They could be like Assasin's, Berserkers and Lizardmen in Soul Callibur, one fighter without his own true identity, that represents a number of fighters in story mode. So, as you defeated these Lin Kuei warriors, you would also unlock new outfits for a character in VS mode, simply known as Lin Kuei Warrior. You may also fight some Tarkatans who had come to Earthrealm to kill you for your acts in MK:D. These would simply be an alternate costume for Baraka. You would also meet up with numerous members of the MK main cast who you would do battle with for one reason or another, but this would give you a purpose for every battle. The game could even give you a briefing, just a few sentences, explaining why you fight each battle.

The game could even make each fight connected, as you would be traveling somewhere. So you might fight on a mountain, and see a forest in the distance which would be your next fight arena, and a volcano to the other side, which is where you came from. But then, when you play as someone else latter, you would realise that temple to the left, is infact, another location for another combatant, and so you would see how these fighters might cross paths. So if Baraka meets with Mileena in one location, then in Mileena's story, she would meet baraka at the same location, but have a different way of getting there, and different destination afterwoulds.

If you were to travel to a portal to another realm, you might also see one in the distance, or fight next to the portal between the realms. After going threw it you might see the portal in the distance from the other side in the next level.

So my idea is to have each characters story their own, rather than playing a bunch of irrelavent fights which the story tells you you could never have done anyway.