Leper C:

 Because the covenant were/are afraid of the humans, soley based on the fact that they are basically forerunners. In Halo: Contact Harvest it explains how the covenant find this out, and basically the 3 prophets in halo 2 agree that they can never tell the covenant what they learned about the humans.

Congratulations! You just reiterated everything that we've already stated! Except you are wrong about a few things.

Humans are not Forerunners, or even basically Forerunners. The Hierarchs decide in Contact Harvest that they cannot tell the Covenant about Reclaimers, not Halo 2.

Leper C:

In the little "Conversations from the galaxy" pamphlet that came with the Halo 2: Collector's Edition, one of the little "conversations" is two elites talking about why the covenant never gave the humans a chance to join them. Basically, it says the same thing. They were afraid. 

The Prophets just wanted power. That is the sole reason they didn't tell the Covenant that the humans they were committing genocide against were 'Reclaimers'. Although they say it may have been to' preserve the Covenant, they were only doing it so that they would have power. After all, they were already plotting to usurp the current Hierarhcs, and it would have been a shame to see all that scheming go to waste.

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Opress the Opressed