The fact that these two close friends will end up bitterly opposing each other, *neither by their own violation*, but as unwilling players in a game between Coyote and the Headmaster?, as well as the parallels that they hold for each other, and possibly Kat for Coyote (remember what the OP was, way way back there?) is heartwrenching but a beautiful story. Like I said, I really wish happy endings for everyone, but if you look at the evidence in the plot (my quote) - it's hardly a stretch by any means, I'm just stating what we see, not what we can infer - there's no way that I can see this ending well. To drop all the foreshadowing and write fluff is shoddy writing, and Tom would not do that. There's a dark plot ahead, I'm certain.
I think there's also an inner thread to each of them that is pulling them to these directions, involuntarily, but not merely as pieces in headmaster's and coyote's plans. Right now, the conflict is building up according to the plans of these current antagonists, Headmaster and Coyote, and Kat and Annie don't even realize they are slowly being pulled apart to opposite sides. But I can see them ending up as the main players of this conflict in the end, and the original antagonists suffering badly in the course of action and even being overthrown from their current positions. There seems to be much uncontrollable in these two characters, and to me there is a fair and dramatically interesting possibility that they will precisely slip out of control of the current villains, massively cross the borders of the plans and cause mayhem way beyond anything that Headmaster and Coyote had imagined, turning their worlds - both of them - inside out. Something in these lines is what I think it might end up being.
But so far that is just a dramatically seducing possibility in comic. I cannot possibly signal any particular cue in it that would justify conclusion that it would go that way. It is merely a feeling I get when looking at Divine, Kat's robot projects and Annie's growth into a serious force. It is, in fact, more Kat than Annie who makes me think they will go absolutely crazy, but this is Annie's story and I have no doubt in my mind that she is someone very special in this world and ends up playing a huge role, much bigger than part of other people's (or God's) plans.
"We cannot tolerate the proliferation of this paperwork any longer. It is useless to fight the forms. We must kill the people producing them."
- Attributed to Vladimir Kabaidze, Director of the Ivanovo Machine Works near Moscow, in a speech before the annual Communist Party Congress, 1936
Hey, I have something ontopic, will I be hung? Anyways, Coyote said that Gunnerkrigg Court was "man's attempt to become god", which everybody decided was entirely confusing - shucks, it's even the TvTropes quote - but if Kat does become worshiped by the robots, she will complete that prophecy, and not even metaphorically! Ironic that the most confusing line from GC may end up being the most straightforward.
I think this theory is great! One note though; I'm a sucker for happy endings, so my theory is going to be something along the lines of "Kat and Annie overcome the forces of their respective sides and forge a unified Court-Forest, as it was when the Court first grew from the Seed Bismuth." I appreciate tragedies literarily, and if Tom goes that way, it will be on par with some of the greatest writing ever, but I'm REALLY REALLY HOPING he doesn't do that. Also, has Tom ever said how long this entire story is going to be?
There's something you better understand about me 'cause it's important and one day your life may depend on it...I am definitely a mad man with a box!