In 1961, at the age of 70, Stephenson was arrested in Independence, Missouri on charges of attempting to sexually assault a 16-year-old girl but he was released after paying a $300 fine because the charges were dropped on grounds of insufficient evidence. He was ordered to leave Missouri immediately. A few years later, in 1966, Stephenson died at his home in Jonesborough, Tennessee, and as an honorably discharged veteran was buried at the USVA Mountain Home National Cemetery in Johnson City, Tennessee. Congress later passed restrictions barring serious sex offenders or those convicted of capital crimes from burial in veterans' cemeteries.