I have some ideas....this is gonna be a long post lol...
1) There's a struggle for power in Outworld after Shao Kahn is killed. Mileena ends up in a fight with Baraka & loses. Mileena leaves Outworld & Baraka ends up essentially replacing Shao Kahn as leader of Outworld. Rain replaces Baraka & is given control over the Tarkatan army, as promised to Rain by Shao Kahn. Sheeva, Goro, & the Shokan try to challenge the Tarkatans, but Rain & his forces completely overwhelm them, leaving the Shokan under Tarkatan control. Although Quan Chi had betrayed Shao Kahn, Baraka's #1 priority going forward is to fulfill Shao Kahn's former goals & invade Earthrealm.
2) During the struggle for power in Outworld, Skarlet is freed by Ermac. Ermac isn't controlled by Shao Kahn anymore so he's good now. Skarlet wants to get revenge on Quan Chi for betraying Shao Kahn. Ermac, realizing that Quan Chi needs to be killed, follows her into the Netherrealm. They run into Scorpion. After Skarlet defeats Scorpion alone, Ermac reveals to Scorpion that Quan Chi killed his family not Bi Han. Scorpion now decides joins Skarlet in focusing solely on killing Quan Chi, but they are ambushed by Shinnok's forces & are forced to retreat.
3) Badly injured Mileena runs into Havik, who heals her injuries. Wanting to spread chaos Havik opens a portal for Mileena to Edenia. Since Edenians have no knowledge that Kitana has been killed, they mistake her for Kitana which allows her to have control over the realm. Shortly afterwards, Ermac separates from Skarlet & Scorpion to assume the role of King Jared in Edenia (his Mk9 ending). When he arrives, he is greeted by several Edenians who quickly recognize that he is indeed King Jared, & take him to "Kitana". Upon entering the royal chamber, Ermac is shocked to see Mileena as princess of Edenia. Mileena quickly tells all the guards to leave, and fights Ermac. Although Ermac wins, Havik shows up & threatens to revive Shao Kahn if Ermac reveals Mileena's secret. Knowing that he will once again be a puppet of Shao Kahn, Ermac is forced to let hide Mileena's secret & pretend to be her father.
Tanya makes an appearance as a lead warrior for Edenia. She suggests that Quan Chi & the Brotherhood of Shadow are planning an attack & that Edenia needs to make the first strike. Both Ermac & Mileena agree, & they enter the Netherrealm along with an Edenian army. While traversing the Netherrealm Tanya (who mistakes Mileena for Kitana) attempts to strangle her. Ermac uses his powers to temporarily immobilize her, & Mileena then has a fight with Tanya. Ermac & the Edenian army are ambushed by the Brotherhood of Shadow lead by NOOB SAIBOT....who's alive somehow (he's too boss to stay dead)! Unbeknownst to everyone involved, Quan Chi is observing the fight from a distance. Mileena beats Tanya & Tanya ends up fleeing. Although almost all the Edenians are killed, they end up winning the conflict & Ermac defeats Noob Saibot. Ashrah then shows up & defeats both Ermac & Mileena, but chooses not to kill them. Upon Noob regaining consciousness in Shinnok's spire, Ashrah lies telling Noob that she was defeated. Quan Chi appears in the room exposing Ashrah's lie & uses his powers to teleport Ashrah to a remote section of the Netherrealm to be executed. Ashrah then happens to find the holy weapon kriss. Brotherhood of Shadow members surround her, but Ashrah defeats them. Ashrah returns to Ermac & Mileena, who are just now gaining consciousness, & offers her alliance. Ermac, who realizes Ashrah could have easily killed them, accepts. Mileena then decides to turn good since Ermac saved her life, though she still wants him to keep her secret. The three return to Edenia.
4) Human Sub Zero wakes up materialized in the Chaosrealm. Surprised by his current state, Sub Zero notices Sektor in the distance. Sektor approaches & explains that the Lin Kuei had forgone loyalty to Outworld after Shao Kahn's death in favor of serving Havik in Chaosrealm. In exchange for their services, Havik will revive Sub Zero & Smoke to be the 1st subjects to an improved cyber initiative. Sektor mentions that Smoke is currently being converted, & that Sub Zero is next. Sub Zero tells Sektor that he must think for himself instead of following the Grand Master's wishes. Sektor then tells Sub that he slayed his own father, thus making Sektor the new Grand Master. Sub Zero fights Sektor, wins, & escapes to Earthrealm. Cyber Smoke ends up being successful & serves under Sektor in Chaosrealm. Sub Zero eventually joins Raiden's group in Earthrealm.
5) Bo' Rai Cho is training in a remote location in Earthrealm when a heavily wounded warrior approaches slowly in the distance. Bo' Rai Cho aids the warrior, an Edenian who tells him that he was nearly killed by Brotherhood of Shadow. Bo' Rai Cho senses good his new acquantance & offers the Edenian his training. He accepts & spends several months training under Bo' Rai Cho. Several times during this period Raiden, Sonya, JC, & Kenshi observe his training sessions. Kenshi senses something familiar about the warrior, but keeps it to himself. At the end of the training session, thanks Bo' Rai Cho, says his goodbyes, & leaves for Edenia. As he's walking toward the distance, his hair color grays slightly & his height varies. When he enters Edenia, he runs into Mileena & claims to have been held captive by Rain in Outworld. Mileena believes his story and accepts him into her realm, but is surprised by the casual tone in his voice, as if he knows her personally. Little does she know that the unknown warrior is Shang Tsung in disguise, whose goal is to stay hidden until he can take control of Outworld from Baraka.
So I'm thinking we'll have something like this
Earthrealm - Raiden, Sonya, Johnny Cage, Kenshi, Bo' Rai Cho, Sub Zero
Outworld - Baraka, Rain, Reptile, Sheeva, Goro, Kintaro
Netherrealm - Shinnok, Quan Chi, Noob Saibot, Tanya
Edenia - Ermac, Mileena, Ashrah, Shang Tsung (hidden)
Chaosrealm - Havik, Sektor, Cyrax, Robot Smoke
Neutral - Scorpion, Skarlet
Plus any other characters people want
