I agree with you Sally and I loved reading the "witch" in the system part of your story line! It was great!

I believe the scientists are undermining the Church through aiding the resistance, because they want to take over Earth! They firmly believe they can do a better job and that no religion is the correct and level headed way to lead a colony, let alone an entire planet.

I like that a lot.

But does the re-appearance of the moon affect their plans somehow. Does it kick start them into overdrive? Does it ruin some of their plans? Or is the re-appearance incidental?

If they knew that the Moon was coming back, as DG suggested, then all the sabotaging going on could have been in preparation for the moon's arrival -- all diversions so that no one sees what the scientists are up to. On Earth, the Church and EA are in chaos (with the leaderships of both groups taking hits). The Rebellion is ready to strike. Things are askew on Mars and in the asteroid belt. And now the scientists have some sort of virus that kills.

It's interesting how the scientists are softening up their competition, not realizing that they may be leaving the solar system defenseless against the Elpins.

I kind of like the Inquisition idea. The world is in choas after the moon disappears, and it is unlikely that the Church came into power right away so I would see a clash between the two and maybe the church gains the upper hand by blaming the scientists for all the ills in the world (like they do now) and because of the Church's prophecy they wind up with the majority of the population on their side and the scientist who think they are there trying to helpo are run out of town on a rail and the chasm between the two widens,. THe scientist slink out and regroup had restart their idea of a perfect society elsewhere hidden for all these years and its only been like in the last 100 years that their power base has become strong enough to allow them to try and swing the balance back their way.

I think there needs to be something in the far past that sets the scientists back. Maybe Hebe Station crashing to Earth made the scientists lose many years of research (and many members). (Maybe someone sabotaged the station). Maybe when the Church gained power early on, they had themselves their own little Inquisition and went about systematically dismantling (and killing) those who might oppose them (like the scientists) and ultimately drove them underground. Maybe the scientists' own experiments caused their own downfall, culling their numbers and forcing them to isolate themselves. Maybe it just takes them a really long time -- 1,000 years -- to get all the right pieces in the right places. (Maybe that last piece they need is on the Speedwell ... or is the Speedwell).