Johnny Cage defeats Shinnok in the Netherrealm War. Raiden imprisons him in his amulet.
25 years after MK9:
For some unknown purpose, Cassie and her team seek out Sub-Zero. He knows them by name. Sub-Zero mentions that they are not ready because they lack cooperation ("you lead, but they do not follow"). Part of their arcs will be learning to work together. Apparently, Cassie fights Sub-Zero to prove her worth.
Later, Cassie and her team arrive at the Spec Ops base and learn from Li Mei that Mileena has the amulet and is causing Kotal to become desperate. How did Mileena obtain the amulet, I wonder? Raiden seems to be advising the young spec ops team.
They go to Outworld and are escorted to see the emperor by Erron. Cassie claims Kano spilled Kotal's secrets to Mileena. Cassie also tells Kotal about Mileena and the amulet. Kotal questions Kano about Mileena's location while riding in his wagon.
Mileena ambushes Kotal on the streets. Rain helps her during the fight.
At some point in Outworld, Takeda, Jacqui and Cassie are captured and thrown into the brig at the Kove. Some shaolin monks are also escorted into the brig, but it's not known if this is a separate occurrence. Someone who appears to be in disguise probably gets them out (Kung Jin is the only one not shown captured). They escape and plan to attack their guards, Ermac and Reptile.
Later on, back on Earth, the team sees an unknown entity erupt from the shaolin temple. It soon envelops the region in a blood red cloud. Kotal's army arrives there as well and surround Cassie's forces. A revenant Sindel and Kitana guard the shaolin temple. I believe Liu Kang is involved here.