Afterwards, I've mentioned it to others and they've all said they thought that flying the flag upside down was a sign of disrespect, even my Dad who served 20 years in the Army. My immediate thought was danger until reason kicked in. Guess they don't teach soldiers the same things they teach Marines.
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I thought it meant disrespect too.
My first thought when reading your post was that you stumbled upon some kind of Waco militia rebel town.