This term also is a nautical term as with most of the sayings we have today. In vessels such as large ships some people may feel discomfort or just get sea sick due to the rolling of the waves and the swaying of the ship when they are topside or on the deck. Some relief can be found if they go below deck into the bowels of the ship where the waves are not visible and the vessel does not sway or rock as much because of the way the vessel sits low in the water.
When people do this they are said to be under the weather because the weather or the outside is not visible and they are separated from it by the deck of the ship and are in a more stable position.
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