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Why did the prophets begin the genocide of humans?

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This is because humanity was designated by the Forerunners as the 'Reclaimers', the heirs to the Forerunners' technology and territory. In the Covenant, where the Forerunners were worshipped as gods, this would make humans second only to the Forerunners themselves, which made them a threat to the Prophets' power over the Covenant. So the link between the two was hidden and humans were designated 'unclean', to be destroyed.

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