i formed a theory that cuccos are like killer bees, they swarm you if you piss 'em off and the only way to escape them is by submerging yourself in water (like the well in kakario village in OoT) or running indoors

Well, I like the way it works in TP. If you beat on one of them enough, you can control it. Link's sweet revenge.

Submerging yourself in water will NOT save you from killer bees. They simply wait for you.

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Heaven sends me here to you
And if a-you fear you've reason to
Open up all seven seals
The beast is come to claim the youth