At the outbreak of secession, Stone found himself in Washington writing his report on Sonora. After a dinner with his former commander Winfield Scott, Stone was requested to be Inspector General of the District of Columbia Militia at the rank of colonel as of January 1, 1861, and was thus reputed to be the first volunteer officer mustered into the Union Army before the Civil War. In this role, he secured the capital for the arrival of President-elect Abraham Lincoln, and was personally responsible for security at the new president's inaugural. One of his most important acts in this role was to frustrate an attempt by southern militias and the secret society known as the Knights of the Golden Circle to carry out a coup against the nascent Lincoln administration. Stone received word that militia groups from Baltimore and surrounding areas intended to infiltrate Washington, D.C. and seize the city by force during Lincoln's inauguration. First Stone forced one suspected militia commander to give an oath of loyalty to the United States or be stripped of all rank, upon which that commander resigned. A second commander was maneuvered into handing Stone a full roster of all the men in his militia, then denied access to weapons and thoroughly investigated. Stone's prompt action disintegrated the plot against the inaugural.