I guess we’re getting what’s going on bit by bit. Clearly Fractale is a system that was put in place at least 400 years before the time of the story (since the first episode said something about it being 22nd century technology and Clain tried to use a 26th century algorithm to fix the ship in episode 5) which is used to keep the citizenry docile, though to what end I’m not sure of yet.
We know that Fractale has certain benefits: it keeps you healthy, gives you a guaranteed income, and gives one mobility, but at the cost of basically being brainwashed and discouraging truly intra-personal relationships (as in person-to-person and not through dopples). Lost Millennium appears to be a loosely associated set of groups who all share the general goal of ending the Fractale system. Groups such as Granitz appear to be generally non-hostile, except towards the people who administer the Fractale system, while other groups, such as Alabaster, trick people into disconnecting from Fractale, and then using their helplessness as a means to recruit new members.
Phryne seems to be the real mystery. She’s run away from the Fractale priestesses, though we don’t know exactly to what end, though it seems that she believes that if she and Nessa ran away, it would somehow bring an end to the Fractale system. However, she seems to be somewhat opposite of Nessa. While Nessa has said she “loves love,” Phryne said she “hates love,” though I think she’s lying to herself more than anything when she says that, since she doesn’t seem to mind Clain, and later, Nessa’s companionship.
There is still the mystery of why Fractale is failing and what the priestesses plan to do to fix it, and how that involves Phryne. Also, there is still the question of what Nessa is, exactly, since Sunda seemed surprised that she was still around, even when they were in a zone where Fractale’s signals didn’t reach.