This whole plot of a divine being seeking to wipe out all existing timelines and realms to start everything fresh was actually a pretty good plot. It was a nice change from the "so-and-so wants to conquer the existing realms and rule them" that almost every other game's plot has been except for Armageddon. Some people have said this game is a repeat of Armageddon plot wise but I think there's an important difference in that Kronika wanted to basically hit the reset button on all of existence whereas in Armageddon the intention was to destroy all of reality and resurrect the One Being. All of this being said allow me to go on to the plot that's percolating in my noggin.

After the reset of the timeline that occurred at the end of MK11 but with the good guys in control of the new timeline things have mostly unfolded as they did in the original Mortal Kombat continuity under the guidance of Lord Liu Kang and Kitana with a few differences. Hanzo Hasashi and his family and clan were not killed by Bi-Han and the Lin Kuei. Instead they were killed by D'vorah and the Kytinn at the behest of Shao Kahn because Hanzo was seen as a potential threat to Outworld's winning streak in the Mortal Kombat tournament. As a result Scorpion does not kill Bi-Han in MK1, and Bi-Han does not become Noob Saibot but remains as a Sub-Zero. However Bi-Han is still not a good guy, and his younger brother Kuai Liang took control of the Lin Kuei from him.

The story picks up around the same time as the time jump from MKX. Neither Raiden or Liu Kang defeated Shao Kahn back during the invasion of Earthrealm and instead Earth's champion and savior was Kung Lao. Kuai Liang is still Grandmaster of a reformed Lin Kuei. In response Bi-Han has formed an opposition clan by automating warriors including himself into cyborgs, known as the Tekunin which he leads with his top lieutenant: Sektor. Cassie, Jacqui, Kung Jin, and Takeda all exist as before and Johnny Cage and Sonya are still together in this timeline. Like in the OG MK timeline Cyrax was rescued from the Lin Kuei and had his humanity restored by the Special Forces and works with them. With Kenshi's help and the responsibility of helping to raise and train Takeda Scorpion has gotten control of his rage and thirst for vengeance and resurrected the Shirai Ryu as in the MKX timeline. Sindel did not kill all those warriors during the invasion of Earthrealm and was instead brought to the light by her daughter Kitana, and she now rules a freed Edenia as queen.

Without being able to manipulate Scorpion, Quan Chi was unable to free Shinnok from the Netherrealm. The sorcerer received a vision from a mysterious being residing deep in the bowels of the Netherrealm showing him events from the previous timelines, and giving him a plan of action for subjugating the realms to Netherrealm. Quan Chi is to travel to Shang Tsung's island and save the being of chaos known as Havik from defeat by transporting him back to Chaosrealm where Quan Chi encourages him to spread chaos across the realms and gives Havik enchanced powers including the ability to open portals to whatever realms he chooses.

The Chaosrealm invasions of the other realms begins, and in response to the Chaosrealm invasion of Orderrealm, the Seidan guardsman Hotaru takes leadership of that realm and begins a counter offensive to enforce order across the realms. This is what the forces of light led by Lord Liu Kang and Kitana find themselves faced with at the beginning of the story. Meanwhile at the behest of the mysterious and powerful being within the Netherrealm Quan Chi also reaches out to Goro and Daegon, the leader of the Red Dragon. He promises them that if the Red Dragon aids him by going after the Lin Kuei to gain possession of the Kamidogu dagger with which his boss can be resurrected to life and allow Goro to regrow his lost arms and therefore be able to claim his place as King of the Shokan, and allow Daegon's Red Dragon to resurrect a being who will be instrumental in awakening the One Being: Onaga, Quan Chi's boss (in case you hadn't guessed it).

Liu Kang seeks out Raiden who has been living as a hermit for many millennia not being the protector of Earthrealm, and with the new threat they are facing from the forces of Chaos and Order they appeal to the Elder Gods to restore Raiden's status as Thunder God and allow him to work alongside the Fire God Liu Kang in order to protect not only Earth but the other realms threatened. Meanwhile Quan Chi finds D'Vorah and Reptile, and promises to resurrect the Saurians and give both the Saurians and Kytinn their own separate realms with Reptile and D'Vorah as rulers if they help him. He also recruits Bi-Han and the Tekunin by promising them that the Lin Kuei will be crushed once and for all and he will able to rule his own ice realm full of obedient cyborg subjects. With the convincing of his old friend Nightwolf, Kabal turns on Kano with Nightwolf defeating Tremor and Kabal defeating then killing Kano. Kabal takes control of the Black Dragon in order to lead it (along with Erron Black) in battle against the Red Dragon. And finally, Liu and Raiden resurrect Shang Tsung in a youthful form and show him the great power that his rival sorcerer Quan Chi is about to amass, and Shang Tsung makes it his mission to find and defeat him. He is not now a "good guy" but more like an anti-hero going after Quan Chi for his own personal reasons.

Special Forces and other warriors of light are split between Earth and Edenia defending against forces of Chaos and Order, and a group of each fight them back to their respective realms. Reptile and Mileena (who hates Kotal for having the throne) lead allied Red Dragon forces along with Reiko in attacking Kotal Kahn in Outworld wanting to vanquish him to prepare the way for the return of Onaga but Kotal Kahn escapes alongside his new top lieutenants Ermac and Baraka. The Kytinn launch a brutal assault on the headquarters of the Shirai Ryu killing all but the absent Scorpion and Takeda. The Tekunin succesfully steal the Kamidogu dagger from the Lin Kuei and inform Scorpion who is present that his pathetic clan is once again no more. Scorpion travels back to Shirai Ryu headquarters to find it in ruins and everyone dead, and sees the signs that it was a Kytinn attack. Enraged, he travels to Outworld to seek vengeance. Meanwhile, a group of warriors in Seido/Orderrealm (Cassie, Jacqui, Kung Jin) and a group of warriors in Chaosrealm (Kung Lao, Sindel, Nightwolf) come to final battle against Order and Chaos. In Orderrealm Cassie defeats Hotaru while Kung Jin defeats his top lieutenant (another Seidan and a new character). In Chaosrealm it's Kung Lao who defeats Havik while Sindel defeats his top lieutenant (again, a new character).

Shujinko finally alerts Raiden and Liu Kang to the Onaga threat just as at the same time Onaga is resurrected with the body of Goro as the vessel. In Outworld, Kotal Kahn, Ermac, and Baraka track down Reptile, Mileena, and Reiko and Kotal Kahn defeats Reiko, Baraka defeats Mileena, and Ermac defeats Reptile. Kuai Liang and Takeda follow the Tekunin back to the Netherrealm where they took the Kamidogu dagger which Cyrax has also found his way to looking for his former Tekunin masters. Kuai Liang first faces his old friend Smoke in battle, and then defeats his brother Bi-Han who is killed while Cyrax defeats Sektor.

Scorpion makes his way to the home of the Kytinn in Outworld and faces D'vorah where he defeats and kills her. Shang Tsung finds Quan Chi with some help from his defected servant Sareena and defeats him while Sareena defeats one of his minions, the returning Kollector. The Black Dragon, Kabal and Erron Black, have followed the Red Dragon back into Netherrealm where Erron Black defeats Skarlet who is now Red Dragon and Kabal defeats Daegon's top lieutenant Mavado. Ashrah who has recovered her Kriss uses it to defeat Daegon (the game's sub-boss) in battle.

Liu Kang and Raiden tell Shujinko that despite his feelings of great shame that the events of his life are written in the timeline, and that the mistakes of his youth also make it his destiny now to confront and defeat the resurrected Onaga. Kuai Liang presents him with the recovered Kamidogu dagger and with it's aid he defeats Onaga. Smoke is restored to his human form afterwards, Bi-Han is shown in Netherrealm in a non-cyber form once again beginning to transform, an escaped Sektor is shown beginning the process of manufacturing new cyborg warriors, the Red Dragon are no more, Kabal has disbanded the Black Dragon and joined the Special Forces while Erron Black has gone his own way, Scorpion and Takeda are shown to be rebuilding Shirai Ryu headquarters with help from the Lin Kuei, and Shujinko has joined Kung Lao and Kung Jin in the White Lotus.

Base Roster: Liu Kang, Raiden, Kitana, Daegon, Quan Chi, Havik, Hotaru, Mavado, Kabal, Erron Black, Cassie, Kung Jin, Takeda, Scorpion, Sub-Zero (Kuai Liang), Cyrax, Sektor, Kung Lao, Shujinko, Sindel, Nightwolf, Shang Tsung, D'Vorah, Reptile, Mileena, Ermac, Kotal Kahn, Tremor, Ashrah, Sareena, Baraka, Skarlet, and the two new characters.

DLC: Cyber Smoke, Cyber Sub-Zero (Bi-Han), Reiko, Johnny Cage, Sonya, Kano, The Kollector, Tasia, Li Mei, Nitara, Kenshi, Delia, 2 guest characters (initial Kombat Pack of 6 then two more of 4 each), and the initial smaller form of Onaga (about the size of Goro) as the pre-order bonus for a total roster of 49.