Which one is your favorite?
Sorry if I missed any, I have no prior knowledge of anything but the games (no idea what characters are in the books).
*Reason 343 Guilty Spark was not listed- I didn't exactly consider him a "villain", more of a machine programmed to do what it's supposed to, save the galaxy by destroying the Flood, be that he may have to activate the rings.*
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I honestly have to say, the Covenant are more intimidating. Sure the flood drove the forerunners to extinction, but that's because of the Halo rings. The Prophets have advanced tech and nearly wiped out the ENTIRE HUMAN RACE with it. In fact, Earth would have led us to near extinction had it not been for insurrectionist outposts and UNSC ships out in the deep void that is space. Besides, when the Gravemind speaks, he sounds more like the intellectual super-villain that you'd be able to converse with rather than a truly menacing foe. The Prophets are religious fanatics that wanna kill anyone that disagrees with them, kinda like the terrorists that plague earth today. So in all actuality, which one poses more of an immediate threat? Ya can't reason with the Covenant.