The nether part of something is the lowest part of it, the bottom. If you’re having, ahem, trouble in the toilet, you might want to go talk to the doc about your nether parts.
You might find the word nether in old books where "the nether world" could mean the world under the earth’s surface, like in Dante’s Inferno where he travels through hell, under the earth, before climbing up to paradise in the heavens. If you look closely you can hear the word nether in the word we normally use now: beneath.
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