Four days later, on March 8, 1863, he was captured by Confederate partisan ranger John S. Mosby while asleep at his headquarters in the Virginia village of Fairfax Court House.

Stoughton resigned his regular commission in March 1861, and in September was appointed commander of the 4th Vermont Infantry with the rank of colonel.

In November 1862, he was appointed brigadier general of Volunteers, and he assumed command of the 2nd Vermont Brigade on December 7, replacing Colonel Asa P. Blunt.

Stoughton's appointment was never confirmed by the U.S. Senate and it expired March 4, 1863, less than a week before Mosby's Fairfax Court House Raid.

Stoughton had hosted a party for his visiting mother and sister, who were staying at the home of Confederate spy Antonia Ford.

In his own written account of Stoughton's capture, which appeared in Volume III of 1888's Battles and Leaders of the Civil War, Mosby did not mention the supposed "spanking" incident.

U.S. President Lincoln, on hearing of the capture, said that "he did not so much mind the loss of a brigadier general, for he could make another in five minutes; 'but those horses cost $125 apiece!

[9] Stoughton defended him at his trial; Cobb was convicted and in March 1865 he became the last Confederate soldier to be executed by Union authorities.