I couldn't get to sleep, so I started to think of ideas of what MK can do for the future. I saw some other people's ideas on this forum and wanted to throw my sleep deprived ideas out there.

Main Story:
Years and years of allying themselves with every threat to Earthrealm, and being the punching bag of Earthrealm defenders have finally paid off. Stealing the Lin Kuei and Special Forces technology, picking off Outworld's grunts for experiments, and gifted knowledge by Shinnok, the Black Dragon have completed their underground army of soulless cyborgs to take Earthrealm from the inside. Blindsided by this unforeseen attack the Earthrealm defenders are defeated. But Kano is a soldier not a mastermind, the true leader of this new Earthrealm... Daegon. He gave Kano the mission to create the Black Dragon as a cover so he could gather the secrets and resources of Shao Khan, Shinnok, and Kotal from their side, while the Red Dragon built up supporters in Earthrealm who feared the other realms and felt unsafe with the Special Forces protecting them. All so Daegon could burn Earthrealm to the ground to find Blaze.

The Heroes:
During the Black Dragon emergence many of Earthrealm's heroes were defeated. Kenshi, Jax, and Johnny were killed, and Sonya was captured by Kano. Fujin sensing defeat, sent the young heroes out to find allies in other realms while he himself left to seek guidance from the Elder Gods. Scorpion and Sub-Zero are left on the ground to weaken the Black Dragon with guerrilla warfare.

Cassie - Outworld:
Cassie is sent to Outworld and seeks help from the emperor. However, Frost (who betrayed the Lin Kuei and was Black Dragon since the beginning) followed her and seeks to put an end to the Cage legacy. Cassie finds refuge with Bo'Rai'Cho and his new apprentice Li Mei, while she struggles to find a way to get Kotal to aid her...

Jacqui - Orderrealm:
Jacqui finds herself in a strange new realm. She runs into Hotaru, and after a misunderstanding she finds herself being hunted by the Seido Guard. She is saved by the Resistance leader Darrius. A new and improved Darrius agrees to assist Earthrealm if Jacqui joins the Resistance. Jacqui accepts seeing a lot of her father in Darrius, however she soon discovers he has a much darker side...

Kung Jin - Chaosrealm:
Jin wanders Chaosrealm in search of allies and stumbles upon a certain cleric (of course). Havik refuses because he loves Earthrealm in chaos, however he sees potential in Jin. Havik decides to help Jin only if he can create some chaos. But as Jin travels with Havik, he begins to enjoy the chaos more and more...

Takada - Netherrealm:
Takada is immediately taken in by Kang's forces. Takada pleas to Liu for help, but Liu has washed his hands with Earthrealm and banishes Takada out into the pits of Netherrealm. There he meets Sareena, who tells him about the souls of the Shirai Ryu locked deep in Netherrealm by Quan Chi. He can restore them, but he will have to go through oni, hellspawn, and a familiar face (or lack of a face) from the past...

Side story:
Tayna and Rain are still recovering after their defeat, when Jade appears before them telling Delia saved her soul from Quan Chi and brought her back to save Edenia. They must find go find a dragon egg in Outworld and bring it to Daegon's hidden base where he has imprisoned a dragon named Caro. This will resurrect Argus who will make them all gods of Edenia. However, an old man keeps standing in their way...

Boss story:
When Fujin goes to the Elder Gods, they tell him Raiden is the supplying the Black Dragon's with unlimited energy using the Kamidogu. He has finally lost it and says he's tired of defending a realm that is in constant danger. Together, he and the Black Dragon, will conquer all the realms, so there will finally be peace under one rule (no matter how violent that rule may be). Fujin challenges him to MORTAL KOMBAT!

There is no ending in the Story Mode. Every character's arcade ending tells a maybe/what if ending to their story to get back some of that old arcade ending feel and bring some of the mystery back.