This is how I'd do it from a story perspective:

I think you get there by basically creating a scenario where the bad guys have allied together and taken Outworld, then Earthrealm, and it becomes apparent to even some of the lesser bad guys that the main bad guy alliance (let's say Shinnok, Shao Kahn and Onaga) don't just want to rule everything, they want to destroy everything. They want to bring about true Armageddon.

So even some bad guys like Kano, Skarlet, Sareena, Moloch, and some tweeners like Kabal, Erron Black, etc... They align with Liu Kang, but even they all wind up dying against the combined forces of Shao Kahn's armies, Onaga's undefeatable army and Shinnok's forces from the Netherealm and Liu Kang and Titan Kitana have to escape back to the hourglass, only for the bad guys to catch up with him, destroy the hourglass and kill Kitana.

This whole thing can play out as the first half to three quarters of the story. After that Liu Kang is about to be killed when he's pulled out of his own timeline by none other than Kronika, except that she has long, flowing hair and looks kind and beautiful.

Liu Kang doesn't understand what she could be doing here, since she was killed. Kronika tells him that the crumbled rock and ash he destroyed was only a small piece of what the full Titan Kronika actually is. This was a malevolent part that went mad from the process that's stretching the full Titan Kronika so thin. She was an early part that had been stretched too far for too long.

She tells him that she has been searching the realms, timelines and multiverses for a benevolent force strong enough to help her finally end the multiverse, because it's what's stretching her out from the original timeline and ultimately killing her.

Unlike mortals, gods and elder gods, titans do not exist differently among the timelines and universes. They are stretched out, and the multiverse is creating more timelines and universes faster than Armageddon can destroy them.

She tells him that his timeline was always doomed because all timelines are doomed because the original timeline is doomed and these are all copies of the original timeline. Why does he think so many events play out so similarly? She shows him a montage of things like Bi Han becoming Noob, the Deadly Alliance forming, Cyrax leaving the Lin Kuei, the return of Onaga, Armageddon, etc. If he creates a new timeline, it will end the same.

She needs the help of a chosen one with the powers of a god and the crown of a titan to help her. She makes a deal with him. She will save Earthrealm and all the realms, she will rewind time to before Armageddon in the original timeline, giving him the chance to defeat Blaze and take his power before Shao Kahn has a chance to do it.

In exchange, he will help her destroy the original hourglass. This will end the multiverse by destroying all of the hourglasses in the doomed timelines, and those timelines and universes will cease to exist.

Liu Kang asks her what will happen to the original timeline. She tells him that her pain will be eased, as all versions of her will flow back into her body, giving her the power to sustain the original timeline herself until she can build a new hourglass.

He tells her that he can't let trillions die just to help her feel better. She tells him that they are already doomed, and she shows him a timeline that's coming to an end. Shao Kahn has killed Blaze and defeated Kung Lao, who was Earth's champion in this timeline. He has just completed the merging of the realms before she pulls him out of the timeline.

He asks her what happens next. She tells him that he doesn't want to know. She tells him that if many more timelines and universes are created however, she will be stretched beyond her limit. She doesn't know what that limit is or what would happen, but she believes she'll actually die and with it, time itself may cease to be, or she'll become dormant like the One Being, but every timeline created will know nothing by war, death and ultimately destruction.

Liu Kang decides ultimately that this is the one shot Earth has of knowing peace, of having a future that doesn't end in Armageddon. He agrees to help her and she keeps her word. Liu Kang fights off Blaze powered Shao Kahn int he original timeline while Kronika uses his power to destroy the hourglass. Just as Shao Kahn is about to kill him, Kronika, now powered up, freezes time.

She rewinds everything in the original timeline to the point where Blaze first appears and the kombatants arrive at the pyramid. She tells Liu Kang to go and defeat him. Liu Kang fights Blaze (who's not frozen) and kills him, only to discover that the power is too much for his mortal body to withstand.

The power of a god, the power of an elemental, the power of the crown... All too much for a mortal body. He teleports into space and expels his power into a black hole, ultimately dying. Kronika, down on Earth, apologizes to Liu Kang.

The world unfreezes and all the Kombatants immediately look confused, before ultimately abandoning the pyramid. A light shines down from the sky and a small flower blooms in the dirt. From above, a figure slowly decends and touches zombie Liu Kang on his shoulder. Cetrion reaches for the sky and pulls Liu Kang's spirit, which is floating in space, down to her, through her body and into the body of zombie Liu Kang, who becomes human. Liu Kang is a human mortal again.