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When food, wood, or another substance rots, or when something rots it, it becomes softer and is gradually destroyed.
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If there is rot in something, especially something that is made of wood, parts of it have decayed and fallen apart.
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You can use the rot to refer to the way something gradually gets worse. For example, if you are talking about the time when the rot set in, you are talking about the time when a situation began to get steadily worse and worse.