Athena's hatred for Medusa stems from different accounts in Greek mythology, but the most common and significant reason involves the desecration of Athena's temple.
While there are differing versions, here's a breakdown:
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Medusa's Beauty and Defilement of Athena's Temple: In Ovid's Metamorphoses, Medusa was originally a beautiful priestess of Athena. Poseidon (Neptune in Roman mythology) raped Medusa in Athena's temple. This act of defilement angered Athena.
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Athena's Punishment: As a result of the temple's desecration, and in some accounts, due to Medusa's boastfulness about her beauty surpassing Athena's, the goddess transformed Medusa into a Gorgon. This transformation gave her a hideous appearance with snakes for hair, and the power to turn anyone who looked at her into stone.
Essentially, Medusa became a victim of circumstance and divine wrath, punished for an act she did not instigate. While some accounts suggest Medusa may have angered Athena due to vanity, the core reason for Athena's hatred lies in the violation of her sacred space.