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This is very confusing, why would the Disease Department in The Maze Runner unleash a deadly and painful virus when there could have possibly been other ways to control the human population? like executing criminals and stuff like that? and why did the combined governments agree to it when they know that they are risking wiping every trace of human life out of existence?

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Why does any government produce a genocidal weapon really?

The reason that a virus was chosen is because it was supposed to be a controlled way to quickly and painlessly kill a significant portion of the population, without arousing suspicion or cause panic. A pandemic that was supposed to come and go, with the virus dying off soon may confuse or cause fear, but wouldn't cause a breakdown in society.

mass executions would cause the public to rebel. Killing only criminals wouldn't work towards significantly reducing the population to make up for the dwindling food supplies caused by the heat flares of the sun. Nuclear weapons cause too much collateral damage, radiation, and the public of one area would demand revenge.

They wrongly believed that the virus they manufactured would go out, kill a good percentage of the population, then go inert. It's possible with proper genetic engineering (in real life), to produce bacteria or viruses that die after a few generations. They 100% believed there was no chance for the virus to mutate and wipe humanity out of existence. They were very wrong.

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