If your ancestor left the US military before his Civil War term was up, he likely was charged with desertion. Some deserters later appealed this charge, particularly as pension laws became more liberal and would qualify him for a pension–if he had not deserted. Even if their appeal to change their discharge was denied, information contained in the file may provide additional details about your ancestor and his life during the Civil War and after.
These records are at the National Archives. 
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2 Responses
Actually, his records show he went AWOL from Alcatraz Island which was a Fort protecting San Francisco Bay during the Civil War. He left twice I believe but they took him back each time and he finished his time out there.
Beverley–to whom are you referring? The man shown in the image returned to Illinois where his parents lived.