This almost felt like a series finale. It does raise the issue of where is this series going in the long run? Is every 13 episode arc going to be about Moloch's latest plot that gets foiled at the last minute? Will we eventually do away with Moloch and move onto to another Big Bad?
I very much suspect it'll be the latter. Keeping Moloch as the permanent big bad after all this would be like the Scoobies (BtVS) spending seven seasons trying to defeat the First. I don't think they necessarily have to destroy him, just sideline him for a while (or nerf him).
They could develop a series spanning villain or villainous faction, ala Angel (WR&H), the X-Files (the Colonists/Syndicate) or Game of Thrones (The Others/R'Hllor), etc. Someone or something that's high up on the evil food chain, but whose ultimate agenda is played out indirectly via lieutenants (or evil rivals) each pursuing differing strategies to realize it. Like an Antichrist or some other Abrahamic/Canaanite evil.
Whoever it is, their overall agenda should still be bringing about the apocalypse in some fashion, as its prevention is the whole purpose for the existence of the Witnesses. Adding whole other conflicts would be stretching and diluting the premise.
This would also entail the eventual addition of other "Big Goods" besides just the FF to help the Witnesses with the new threat. Some of these could be other long-dead, historically "redefined" figures. There's still a large well of Colonial-era people and organizations to draw from.
Ultimately, it matters only tangentially exactly what shape the future apocalyptic evil takes, so long as it's not stupid or boring.
