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?
If one is smart, they would get the sheep to fight the resistance.
Then, offer a pre-planned "saviour" solution.