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I think hydras get either a full round attack or one combined breath weapon attack (with one save). I don't think it gets a ton of breath weapon attacks like Tiamat.
But not consitant with the text of the breath weapon.
I too now think each head launches a 3d6 jet with a seperate save. 1st example
The way the text actually works out though, is all the heads breath a single jet dealing 3d6 points of fire damage per head the hydra has. 2nd example
If the hydra was supposed to have multiple jets, the wording of the text "Each jet deals 3d6 points of fire damage per head." would have the breath dealing thermonuclear damage if the jets all overlap. 3rd example
I interpret it as multiple 3d6 jets. Good thing resistance applies to each separately.
But to speed things up, I have each player roll just once and apply that result for the saves of all breath weapons aimed at him. I am pretty sure each has to made separately.