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Originally Posted by eris_sama
I think the hive mind and all the villagers going insane was an excuse to destroy the villagers or rather the pathogen and the evidence of experiments. Maybe the organization deemed the project was a failure and they couldn't harness its power or they already achieved what they set out to do.
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I think I've puzzled out the motive, and if I'm right it's not what I expected. Originally I thought the same as you did, but after reading the QnA thread I noticed KJ's comments on the mastermind (Takano's) motive:
Basically judging by what was said there, the 'queen' thing is just a flimsy justification and Takano pretty much wants to exterminate the village for entirely personal reasons, and came up with the queen theory so that she could persuade the military guys to go along with it.
The 'become god' thing in the TIPs was obviously adressed either to her or a descendant of hers, presumably from the original Dr Takano Irie talks about. Judging from that I'm guessing that Takano has some personal grudge against Hinamizawa in general, possibly because of Dr Takano's disgrace, and wants to take the entire village out.
My guess is Takano managed to convince her superiors that wiping out Hinamizawa was necessary, at which point Tomitake and later Irie turned traitor and intended to go public with what they were doing. Hence they were killed off by the other three men in green/grey and Takano. (Which would imply that the decision to kill off Rika was taken at least a few days in advance of the killing, rather than being something Takano did alone and then used as an excuse to get the military to wipe Hinamizawa off the map, unless Tomitake had stumbled upon Takano's plan by accident and then been pinned by her as a traitor or something)
That said there's one flaw in my little theory I can see right away. If Takano really did intend to 'become a god' in the manner the original Dr. Takano described, why get herself killed in the gas disaster in such a way that nobody would find out the truth? I mean from the way the Faded Notebook was worded she wanted something that would get her accomplishments known, but she'd have to know something as big as the Hinamizawa disaster would get covered up. Unless something went wrong after Rika's death it seems nobody ever found out about Takano's involvement in the disaster beyond being one of the early victims, something which will get her name in the papers for maybe a year or two before fading into obscurity along with every other serial killing in history. Guess I've still got some more theorising to do.