Keep the Heroes Out!
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What happens when the Guild deck runs out during Wave 2?
The designer answered this directly, and the rulebook's Heroes Invasion section says the game is won at the end of the second wave.
The deck is not reshuffled. Running out in Wave 2 ends the game at once: you win, or lose if the scenario says so. Heroes still active resolve first, and every hero must be exhausted before the win counts. If the final cards are Executioners, resolve their effects first.