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All these ideas rely on Quan Chi and Shinnok's clone splitting up the dead evenly who are under their control. I assume that the conquest of Earthrealm and Outworld happen simultaneously and their Netherrealm army is shared between the two leaders. I also have a presumption only the Elder Gods can give another chance at life or evil magic can only resurrect the dead properly without negative consequences.

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For the Black Dragon faction, Kano can lead his own defensive against Quan Chi and his invaders. Kano thawing he gathers his followers (Tremor cameo perhaps?) and attacks Quan Chi for not only ruining the Black Dragon's trading opportunities with Shao Khan, but also to defend his criminal territory and to reclaim the lost soul of his friend Kabal. Despite Kabal being a defector; Kano values him as a previous member of his organisation. The Black Dragon suffers heavy losses to Quan Chi but Kano manages to faces off against the demon personally. Kano blackmails Quan Chi at knife point to revive Kabal; Quan Chi releases Kabal to save his own skin. The elimination of any remaining Black Dragon continues after Kano abandons the Black Dragon's lair with a weakened Kabal.

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Rain created meat as his underling to protect his own interests. Shang Tsung's soul is not under Shinnok or Quan Chi's control; so the Shadow Priests harness their power to revive their leader or previous member. Rain's ability to recreate earthly bodies as shown with meat aids the process. Shinnok's fighters are well matched against the Shadow Priests. The priests fail to hold the line and the enemy troops charge to the top of the "Evil Monastery". I want to see the time factor taken into account. Hours pass before the clone's advancement cut down the chanting Shadow Priests and the clone kills Meat. Old Shang Tsung regained consciousness and opened a portal to his Island. Rain carries Shang through the portal. Undead Sindel manages to go through the portal as a mindless zombie ordered to kill all opposition. Raiden sees this new change in events and teleports to the island. Rain and Shang combine forces to defeat Sindel; just as she is about to be drained by Shang to revert to his young body, Raiden intervenes offering an alliance to the sorcerer. Shang forgets resentments to the queen and accepts. Much to Liu Kang's disgust Rain works with Shang to purify Sindel behind closed doors while guarded by loyal "Mask Guards". If Liu Kang is alive that is! I think this is a great way to build more tension between the Thunder God and Earthrealm's greatest warrior who is already disillusioned. If Liu Kang still ends up as a zombie, then Raiden can offer revenge to Shang and power to Rain just like the arcade endings.