Why did God give mankind free will only to then kill most of them in a flood for not doing things his way?

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God killing people is not the same thing as you or I killing people. God has the benefit of omniscience, which allows him to determine what is just, and omnipotence, which allows him to determine exactly how His plans are carried out.

God can end people’s lives in various ways. I was moved to tears recently when I saw that a wonderful mathematician and his wife died together in a car accident. Personally, I can’t think of many better ways to go. Dying with your spouse is a great luxury, nobody has to spend any time grieving as a widow. and dying without an extended period of time under control of the medical establishment is yet another rare but delightful happenstance.

God can also reward the deserving in the world after, people losing their lives in this world need not be considered a great loss. Naturally only those who believe in an afterlife or try to live in a particularly spiritual way will see things this way.

So God wiping the slate clean and restarting is more scary than it needs to be.