Theory regarding the Faction and last episode of season 1 (spoilers)
In the season 1 finale, we are told that after preventing Helios 685 the Travelers created a new timeline where a faction fights against the director deciding humanities fate. So in this episode Grace informs the team about the Faction and war in the future, the team is unaware of the Faction(due to altering the timeline), and Grace also states that it was the Faction that abducted the team in Episode 5 "Room 101." If you listen to that whole dialogue at the end of Episode 12 "Grace" it would appear as if the Faction was only created after the team prevented Helios 685; however, Marcy, Carly, Trever,and Philip were abducted in Episode 5 and Helios 685 wasn't prevented till the next episode.
So the question is who abducted Marcy, Carly, Trever, and Philip in episode 5 if the Faction was only created after preventing Helios 685? My theory is that it was the Director sent back in time in the season 1 finale who kidnapped them. We know the director is able to send itself and others back in time and if the timeline was altered then the director would not be aware of the teams original mission (to prevent Helios 685). Furthermore, Grace reset the Director prior to the Director's arrival in the 21st Century. This could help explain why the monitor kept asking "what is your mission" and "when are you from" in the abduction episode.
The question then became how could the Director exist in the future if the reason for its existence was to prevent Helios 685 (which was prevented)? The Director was programed to be God and therefore would need to exist in every scenario. Therefore, it would need to calculate both a means to prevent Helios 685)and also maintain its existence and survival in an alternate timeline.
Another theory I have is that Grace was actually on the side of the Faction and the little girl was on the side of the director. The show went out of its way in the last two episodes of season 1 to illustrate Grace's human emotions through an abundance of overacting. I found it annoying at first until I saw the juxtaposed lack of personality and emotion of the little girl after she was taken over. The little girl was robotic, like a terminator or agent from the Matrix.
I think the missions the team received after Episode 6 came from the Faction in an effort to prevent the director controlling the future of humanity. Grace and Ellis's missions was to save the future by resetting the Director and bringing it to the past in an attempt to control it and guide humanity to a brighter future. However, this had the opposite effect and only created that which they hoped to destroy.
Let me know your thoughts.