What is going to happen is that the survivors from the dauntless are going to form a group called "The Order of Restoration". Their goal is to restore the timeline to what it was before they got stuck in all of this.
In the main game, you as the player make all kinds of morality choices and you run into these guys. You will run into Carol Everson and Archer and all them in the main game, and based on your decisions they will either be neutral, or join you, or fight you. It will be good!