While I had some eyebrow-raising moments about the story being set in a classroom, I had no problems with the rest of the story. It wasn't particularly memorable, but it was well put together. To address some issues:
The MC was a great candidate for many reasons. He was motivated to work for his country, but not intelligent or driven enough to be a useful member of any agency. He was VERY malleable, as most teenagers are. He had no connections other than his parents, who would understand obligations and secrets, and wouldn't ask many questions. Most importantly, he had the right biochemistry. I don't think that the government spent boatloads of money searching for the right candidate, I think they had "plague-spreader" on their loooooooong list of projects, and the MC matched the requirements, so they went ahead.
- Why did he care about the boy in Zaquitos and not the thousands of others that he killed?
Because that's what humans do. That's why we care more about the death of the family dog than the death of tens of thousands in a genocide in Africa. Our brains just can't cope with that scope, and refuse to process it most of the time. He found a personally relevant attachment to the boy, and therefore felt obligated to save him. It also internally absolved him of the deaths of the thousands of others, and more importantly(to him) the death of the pretty girl in St. Whatsit.
- Why would the government do this?
Because like the MC at the end states, the government has plans like this in the works ALL THE TIME. Maybe not all of them to this scale, but there are some crazy/devious/insidious plans in the works all the time because they need to be prepared for various contingencies. Go read about some of the wacky Cold War and nuclear defense systems. Or look at things like mustard gas and napalm. Those are atrocious, yet very effective weapons.
- Why use a person when you can use fleas and/or rats?
Because the person is infinitely more controllable.
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