Still confused about a lot things but Mortal Kombat isn't known for having coherent plot lines. Kronika wants to fix the current timeline, so she recruits kombantants from the past to square off with the present ones. Reptile, Mileena, Smoke, Stryker, and a few others aren't apart of this. Also, Kronika probably could have gotten away with it, if she didn't do that. Kronika and Geras can stop present time, so she doesn't really need henchmen. Kronika wants to create a world without Raiden and I believe this makes Raiden jealous and tries to turn everyone on his side by saying she wants to resurrect Shinnok and keep the realms fighting each other. In the good ending with Liu Kang, Kang states it will be up the realms to control their fates, which means there will also be chaos and mortal kombat.