In the fall of 1811 he rejoins the army at department headquarters at Baton Rouge, Louisiana, having made the journey by land over a new road through the country of the Creeks and Choctaws. This winter of 1811–1812 he is appointed superior judge-advocate for the trial of a prominent colonel. He also serves upon the staff of Brigadier General Wade Hampton, commander of the Southern Department, and is much in New Orleans. The inactive life of a soldier in peace palls upon him. In February, 1812, the news arrives that Congress has authorized an increase of the regular army by 25,000 men. This looks like war. May 20, as a member of General Hampton’s staff, he embarks with the general for Washington. Upon entering Chesapeake Bay their ship passes a British frigate standing on and off; in less than an hour they pass a pilot boat bringing to the frigate the message that the United States has declared for war with Great Britain. Thus by a narrow margin they have escaped capture by the frigate. July 6, 1812, is appointed lieutenant-colonel, Second Artillery, at the age of twenty-six. Is ordered with his regiment to the Canadian border; reports at Buffalo October 4, 1812. On October 13 leads 450 regulars and militia in a final attack upon Queenstown Heights, opposite Lewiston, New York. The Heights are held by a greatly superior force of British regulars and militia and 500 Indians. The United States militia left on the American side of the Niagara River refused to cross and support, and the attack failed for lack of reinforcements. There were no boats for retreat; two flags of truce had been unheeded; with his own hand young Lieutenant-Colonel Scott, tall and powerful and wearing a showy uniform (“I will die in my robes,” he said), bears the third flag forward into the faces of the raging Indians to save his men. He is rescued with difficulty by British officers. After the surrender he is held prisoner with the other Regulars until paroled on November 20 and sent to Boston. In January, 1813, is released from parole. Is ordered to Philadelphia to command a double battalion of twenty-two companies. March 12, 1813, promoted to colonel, Second Artillery. March 18, appointed adjutant general, rank of colonel. May, 1813, appointed chief of staff to Major-General Henry Dearborn on the Niagara frontier, New York, and reorganizes the staff departments of the Army. May 27 commands the advance again in the attack on Fort George, Canada. Every fifth man is killed or wounded. By the explosion of a powder magazine his collar-bone is broken and he is badly bruised; but he is the first to enter the fort and he himself hauls down the colors. July 18 he resigns his adjutant generalcy in order to be with his regiment as colonel. Leads in several successful skirmishes.