I expect more revelations yet to come (although I will not be surprised by an ultimate lack of full disclosure), but having just watched Outbreak, my thinking juices have been stirred.
*Super Spoilers*
What caused the outbreak? Owing to its name, it is more or less understood that the Sand Plague comes from ore deposits under the ground. But these deposits are deep enough not to pose an immediate threat to surface dwellers - so how did the disease enter the town? There are a number of possibilities, but what actually happened? And who was patient zero? The accepted explanation, via the Bachelor's scenario, is that the construction of the Polyhedron is what put the town in danger: by drilling a structural support deep into the earth, the ore deposits were dislodged and the disease rose from the depths. But where did it first come into contact with the people of the town? If it had infected the water supply, one would have expected the outbreak to be more widespread across the town, but it clearly originated and spread out from one spot - Isidor Burakh's house.
But, curiously, Isidor Burakh was not killed by the plague. He was murdered by the Elder of the Abattoir. But the infection spread from his house. If he was infected before he was murdered, then how come the Elder was not infected? It's true that the Elder himself was a menkhu like Burakh and his son, and as Elder, he had access to the sacred blood of the aurochs - so could he have produced some Panacea of his own to cure himself? I think it's quite possible. In fact, he may have even stole knowledge of the process of creating the cure from Isidor (or his notes) before or after he killed him.
But what of Simon, who had also become infected? Eyewitnesses claim that Isidor and Simon met the night they were both killed. So, did Isidor pass the disease to Simon, or did Simon pass it to Isidor? Rubin, who was a student of Isidor's, was able to create a vaccine from Simon's cells. Did Isidor know that Simon's special physiology - attested to by his apparent immortality - would provide a crucial key to fighting the disease? Knowing this, did he infect Simon, essentially sacrificing him for the good of the town, or did Simon take it upon himself to play the role of martyr? Perhaps he thought he could beat the disease - and, perhaps, he would have if Rubin hadn't converted his body into medicine.
But Isidor knew the means to produce Panacea. He had discovered it previously when the disease showed up five years prior. So why would he feel Simon's sacrifice was necessary? All he needed was access to the sacred blood of the aurochs, and the only way to get it was to go through the Elder. So why Simon's involvement? Unless we disregard rumours that Isidor tracked the disease in from the Steppe, and consider that it was Simon who was patient zero. Which brings us back to the mystery of the conditions surrounding the first human contact with the disease.
And another question I have is: who and what is the true nature of Simon Kain? The Utopists all attest to the existence of magic. The Kain family claims occult knowledge including even necromancy and the ability to contain souls within architectural shells. The popular superstitious explanation for the existence of the plague is that it is a tool of the earth, its purpose being revenge against Simon and the Kains for breaking its natural laws. This opposition would suggest, if we are inclined towards superstition, that Simon is the primary target of the disease, and thus perhaps he was, after all, patient zero.
Why then, did Simon and Isidor meet on that fateful night? Simon would naturally want to do everything he could to beat the disease, and go on outraging the laws of nature, rather than lie down and accept the earth's decree. He must have known of Isidor's weapon against the disease - his victory against the first outbreak was no secret. So did Simon call upon Isidor to inform him of the plague's new arrival, and to procure a subscription for some Panacea? Quite possible, I think.
But why did the Elder kill the one man capable of beating the disease? The two of them were not on friendly terms, and were in the middle of a power struggle over the Order of the Abattoir. It is conceivable that the Elder, suspecting he could adopt Burakh's knowledge, wanted to claim the cure for himself, increasing his power and influence throughout the town, and especially the Order. Still, why let the disease run rampant? The Elder was clearly reluctant to give out help to those who were sick. In fact, the Panacea practically had to be pried from his cold dead hands by Burakh's ambitious son, the Haruspicus.
And what about the turmoil in the Apiary? Many within the Apiary got sick and died, likely even before, or at least concurrent with, the spread of the disease throughout the rest of the town. Could the Elder have tracked the disease in with him, after fleeing the site of Burakh's murder, only to cure himself and leave a great majority of the rest of the Order to perish in sickness? Even for the Elder, this seems excessively harsh. Ah, but remember that Ospina had led a revolt against the Elder! Perhaps, the Elder knowingly subjected the Order to infection, using the plague as a biological weapon to wipe out his adversaries, while stingily keeping the cure to himself...
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