[3] At the outbreak of the American Civil War, Conrad taught at the Georgetown Institute in Washington, D.C., which also bestowed a master's degree on him in 1860.

[4]: 55 Conrad was given a letter of recommendation from General Stuart to President Jefferson Davis to spy for the Confederate Secret Service.

[5]: 93–95 Captain Conrad went to Washington, D.C. with his Dickinson roommate and Phi Kappa Sigma fraternity brother Daniel Mountjoy Cloud and M. B.

[5]: 95 Conrad set up his covert intelligence gathering operation in the large "Van Ness" estate, owned by Thomas Greene, at the corner of Constitution and 17th in the heart of Washington D.C.[6] Greene had helped Conrad earlier, was a known CSA sympathiser, and a close relative of the wife of CSA Intelligence Major Cornelius Boyle.

His wartime exploits included among other things, hatching a plot to assassinate the Commanding General of the United States Army, Winfield Scott, that was vetoed by the Confederate government who feared that the elderly and infirm Scott would be replaced by someone more fit for command; sneaking into the War Office during lunch hour to lift copies of documents describing General McClellan's battle plans for the Peninsula Campaign, a large-scale offensive by the Union Army to capture the Confederate capitol at Richmond from the desk of a friend who was a double agent; and conspiring to kidnap U.S. President Abraham Lincoln.

[2] Conrad served as the mayor of Blacksburg for three months in 1882[11] and was appointed president of Virginia Agricultural and Mechanical College the same year.

[2] He then joined the faculty of the Maryland Agricultural College, resigning in 1890 to accept a position with the U.S. Census Office in Washington D.C. [13][14] He later retired to a farm in Prince William County.