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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Having read Silentium, I have garnered a new appreciation for the Ur-Didact and Gravemind as antagonists. So those two.