Although little-known today, Cooper was technically the highest-ranking general officer in the Confederate States Army throughout the American Civil War, even outranking Robert E. Lee.

Cooper served as aide-de-camp for Gen. Macomb from 1828 to 1836 and, under his supervision, authored A Concise System of Instructions and Regulations for the Militia and Volunteers of the United States.

[7] Cooper served in numerous artillery units until 1837 when he was appointed chief clerk of the U.S. War Department.

[10] On February 5, 1857, his daughter Sarah Maria Mason Cooper (August 4, 1836 – December 15, 1858) married Frank Wheaton, who became a Union Army general during the American Civil War.

Twiggs had surrendered his command and supplies in Texas to the Confederacy (and was shortly after that made a Confederate major general.)

He traveled to Montgomery, Alabama, at the time the Confederacy's capital, to join the Confederate States Army.

Cooper provided much-needed organization and knowledge to the fledgling Confederate War Department, drawing on his years performing duties as Adjutant General of the U.S.

[16] Historian Ezra J. Warner believed that in doing so Cooper was "thereby making a priceless contribution to the history of the period.

Lee wrote to him saying, "To this sum I have only been able to add $100, but I hope it may enable you to supply some immediate want and prevent you from taxing your strength too much.

"[5] Samuel Cooper died at his home in 1876 and is buried in Alexandria's Christ Church Episcopal Cemetery.