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死亡する is also used in place of 死ぬ because the latter is too strong a word. It's used in news articles, announcements, and I think has a slightly official and impersonal feel to it.
From my personal experience, 「亡くなる」 is the most neutral word. 「先生のお父さんはがんで亡くなられたよ」 - "Our teacher's father died from cancer" 「死ぬ」 is a strong word that is usually avoided by polite people, but is used to express emphasis or to deliberately offend. It can also be used to talk about animals. 「勝手に死ね！」 - Literally, "Die on your own!", but is very strong and ...
死ぬ is the general, neutral term for "to die". 他界する assumes particular belief, namely that the person/animal goes to the afterworld. 亡くなる is euphemism.
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