TLDR:
ありがとう comes from ありがたい, sometimes written as 有り難い ("difficult to exist"; 有り = exists, 難い = difficult), so basically "rare/precious/not to be taken for granted," which is why it became "thank you." This is tied to a Buddhist parable where a blind turtle living at the bottom of the ocean pops up once every 100 years and, by some cosmic miracle, manages to stick its head through a tiny hole in a floating log. The idea is that your life, your timing, and even this specific kindness that's being thanked for didn't have to happen, which makes it all the more appreciated.
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(Article courtesy of かめ先生, appropriately enough)
by thinkbee