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Why did the covenant go to war against the humans?
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The Covenant religion was based on a mistranslation (according to Mendicant Bias), rather than allow that information to make its way to the public and possibly destroy the Covenant the Prophets decided to eliminate the evidence (i.e. humanity).
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Correct but it's also said that truth and Regret killed of the last prophets and took their place to enable their plan (which you stated)
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Close enough. LASO Question?