There are only a few context clues for what goes on in the story mode, but here is what I think happens. I think the scene with Liu Kang and Kitana in the NetherRealm happens towards the beginning. I think they see Raiden arrive in the NetherRealm and start plowing through all of the demons. I believe they will decide to grant him audience and hear him out. I think Raiden will recruit them to his side for the central conflict of the story.
Meanwhile, I think Liu Kang and Kung Lao will arrive from a past timeline from before they became corrupted. They will eventually come face to face with their future, corrupted selves and fight them. I believe that the younger, non-corrupted versions will come out on top.
To take a wild guess, I think the two parallels will eventually team up, as Kronika is a common threat between the two timelines.
My guess is that Raiden will also take Sonya, Cassie, and some of their special forces agents to the netherrealm when he seeks audience with Liu and Kitana. I think they will all have to fight off many demons, and possible take on the revenants in Kombat before they earn their alliance.
