system
Given the following post, respond as if you're commenting on Reddit:
human
[Halo]Why did the prophets try to get rid of all of the Elites?

In Halo 2, The high prophet of Truth decided to "promote" the brutes, and have them kill all of the Elites. Why did he do this? The Human-Covenant war was going great for them up until that point. And besides, why sacrifice such a large, trained, experienced, well equipped fighting force? Wouldn't that be a terrible tactical decision?
gpt
The Elites had an almost equal standing in terms of politics, they were technically equals. With the Prophets being the religious leaders and the Elites the military leaders. 

The Elites never fully embraced the Covenant religion, and so when the Prophets discovered the Brutes, who were just as strong physically but far more devout (and so, easier to control) the Prophet of Truth began making plans for them to replace the Elites (Then the prophets would control the faith and the military). When the High Prophet Regret was killed by the Master Chief, Truth used this as an excuse to change out the Prophets guard. This began the changeover which ended up causing the civil war. 

Whether the Prophets overestimated the Brutes or underestimated the Elites, we can't be sure, but we obviously know the Elites didn't exactly leave peacefully and it kind of blew up in Truths face after the flood arrived.