Thursday’s tragedy should serve as a grim warning to the powers that be of potentially darker times ahead if the surcharged rhetoric is left unchecked.
What does be of mean here?
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"The powers that be" is a set phrase, which means:
important people who have authority over others (Cambridge Dictionary)
So the correct parsing of the sentence should read "the powers that be" together. The sentence is saying that
Thursday’s tragedy should serve as a grim warning of potentially darker times ahead to the people in power if the surcharged rhetoric is left unchecked.
As you can see, the "of" goes not with "be", but with "warning". The complement that follows "of" describes the content of the warning and tells you what is being warned. "The powers that be" is the people in power/positions of authority, and is the recipient of the warning, to whom the warning is issued.