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They are built like mazes to annoy the crap out of the games players and to keep evil and/or intruders out. The praying rooms (certain ones like the first 3 in OoT, Dragon Roost Cavern {there is a praying area there, but not at the end} and Forbidden Woods {used to be a temple} excluded) are the boss's lair. They take over the prayer room to snatch anyone foolish enough to pray with the evil there and to optimize the corruption of evil throughout the temple. ~Pgans

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