Wild Mass Guessing for Sister Claire.
Claire is the daughter of a witch.A silly WMG, but Claire adores cats, feels that playing with that one white kitty feels so right, and apparently was found on the eve of the last fight with the witches. After that eve, no witches have been spotted, which one of the Sisters refers to as a miracle. It'd be a nice twist for the new Mary to be of the very bloodline that started the whole war on God.
Gabrielle is not quite an angel...She is a Fallen Angel. The company G.O.D.? Well, Lucifer did want to run the show... Also, arn't some demons described as looking like angels? Gabrielle's visits tend to get Claire into a lot more trouble than she'd normally get into. Also, the fish-people (merpeople?) seemed to be more devilish or fae than anything 'nice'... Also, how many 'names' does Gabrielle go by? The only angel I know of who has many names is a certain Fallen. Which would mean that...
Claire is pregnant with an antichrist.See: Gabrielle is not quite an angel. Now, first things first: "The Antichrist" is not Damien. An antichrist is pretty much a person that says they're a Christian but doesn't believe Christ is God. Following the other "route", the child would be false prophet that would screw up people's faith in God. The later would help the witches get an edge over their terrible losses in the war. The former, not so much. The misconception... yes.
Catharine is Claire's biological mother, and got pregnant with her in the same way Claire got pregnant.There's been foreshadowing and hinting all over the place for the former, but the later would help explain why she, a nun, would have gotten pregnant. It would also create some interesting mirroring between their stories.
The Reverend Mother knows about Claire's pregnancy.I doubt that none of the other nuns have noticed things, and the RM has shown a lot of interest in Claire since the whole Sister Cat thing. Maybe she has access to a prophecy or such that lets her know Claire's preggers with the Messiah, but hasn't shared it with the other nuns for the same reason that Gabrielle warned Claire not to tell any of the other nuns.
Gray And Gray Morality will be an enduring, major themeSo far, the comic's dealt with the Nun Vs. Witch war surprisingly realistically. The nuns clearly aren't evil, and while their enduring Knight Templar and Well-Intentioned Extremist tendencies aren't portrayed as positively, they are somewhat justified - Witches are dangerous, sometimes cannibalistic, and their numbers are returning. That said, Witches are not Always Chaotic Evil either, since we've also seen at least one faction that would rather just be left alone (except for that one guy) and the Witch Hunts involved burtal methods of torture and execution that were just as bad as those that the Witches inflicted. While some important pieces of evidence are missing, such as how dangerous the Witches were to the world at large, whether "G.O.D." was any better (and if so, how much), who started the war and so on, as of this posting neither side is shown to be much worse than the other, and both sides have their sympathetic angles, and Claire's final challenge will be to resolve a conflict that has no true villain.