Everyone figures depopulation is on the horizon.
The question is, which group do you go after?
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Remove the sheep via vaccine because it's easy? but you'll be left with all the ones smart enough to not follow along... are you banking on the smarter ones being able to understand the reasons why or do you just have the means to oppress them regardless?
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Or do you remove the resistance first and save the sheep? This will be more difficult, you vaccinate the sheep and release something more deadly to remove the resistance... But will the resistance catch on early and start to save themselves? But ruling over sheep in the end should be easier, but they aren't the brightest bunch..
How do you think the game will go?
False dichotomy. You can wipe out billions of sheep and still have billions left to maintain the slave society. The mass die off is necessary anyway to serve as pretext for further authoritarian control and the fact that the smaller number is simply easier to manage. The slaves that survive the remote kill shot are preferred stock given that their bodies are highly tolerant to graphene oxide, the foundational component necessary for gradually transhumanizing them them into more perfect slaves. Poke and prod the sheep minds until they are literally begging you exterminate the the uninjected "resistance". Then do it.