This post will have lots of spoilers for Book 2 (Seven Days to the Grave) (don't say I didn't warn you).
My players are reaching the end of Seven Days to the Grave and I'm having some trouble deciding how Davaulus & the physicians will react to what the players have done.
The Setup: The players spoke with Davaulus but weren't buying his claim that he thinks the plauge was started by some were-rats in Old Korvosa, so they decided to sneak in at night. Using invisibility potions and infusions of Monkey Fish they were able to sneak around the Blessed Maiden fairly freely, but on a short clock. One of them made their way upstairs and threw a thunderstone down the stairwell to draw the Gray Maiden guards away from the door and was able to sneak into the Experimentation Ward where the true nature of the Queen's Physicians became apparent. The character grabbed the research notes from the table but was detected in the process. He and the other characters, still being invisible, were able to run away without being seen, and in the commotion break their way out of the back room onto the street. The characters retreated back to a safe location and perused the notes, discovering the secret (the Cult of Urgathoa) of Davaulus and the physicians. They then rested and spoke to Croft in the morning who was able to issue them a few guards to block off the area.
My question: What would Davaulus and the physicians have done in the intervening ~12 hours? They know what was in the research notes and therefore know that somebody (but not exactly who) knows their secret. I'm sure they would either kill the Varisians from the Experimentation Ward or relocate them down into the Temple, but what of the rest of the infected down in the Sick Ward?
I'm tempted to say that they kill all of the infected (and bolster their ranks of undead), and go into lockdown mode now that the secret is out. This makes sense story-wise to me, but 1) it makes the encounter harder and 2) it's a bit of an emotional slap to the players who now know that 60+ people are dead because of a minor screw up on what was actually a pretty decent plan on their part.
As I see it, the second option is that the physician's try to maintain the appearance of being a Hospital as long as possible. This gives them more time to freely move about the city continuing their research, but leaves them a lot more vulnerable.
How about get the Queen (and therefore the Red Mantis) to intervene on their behalf?
Croft's mysterous death would be a problem for the queen (but if the notes can also be stolen, then she could simply ride out the controversy).
I agree - having them kill all the patients does seem like penalizing the players for trying to play smart, and the cultists and physicians might be reluctant to play that card unless they absolutely have to. Or set a timer. They've requested instructions from the Queen, and unless the Party acts promptly they start killing the patients in 24 hours.
I think a more intermediate approach might be for Davaulus to call for reinforcements from the Queen, who sends additional Grey Maidens (ostensibly for crowd control) and/or several Red Mantis assassins to keep a closer eye on things inside. If the Korvosa Guards' presence is detected, Croft could get orders from the Queen to stand down and leave protection of the Blessed Maiden to the Grey Maidens. Getting back into the Blessed Maiden undetected should be much more difficult. Or perhaps they prepare an ambush and leave an apparent hole in their defenses in order to lure back the intruders.