Jan. 19, 1861, he was promoted to captain, and soon after was ordered by General Scott to proceed to St. Louis, Mo., and assume command of the United States arsenal there. It contained at this time sixty thousand stand of arms, several field batteries, a number of heavy guns, a million and a half of ball cartridges, over forty tons of powder and a large quantity of other munitions of war. Captain Sweeny had only forty unassigned recruits under him to defend this vast property, while in the city were over three thousand Confederate minute-men, armed and drilled, to be ready at a moment’s notice. Learning of a threatened attack, Sweeny let it be known that he would blow up the arsenal sooner than allow it to be captured, and he meant what he said. So they did not make the attempt. Sweeny was brigadier-general of Missouri Infantry, May 20 to Aug. 14, 1861; made colonel of Fifty-second Illinois Infantry, Jan. 21, 1862; was brigadier-general of volunteers, Nov. 29, 1862, to Aug. 24, 1865; commissioned major in the Sixteenth United States Infantry, Oct. 20, 1863, and was retired with the full rank of brigadier-general, United States army, May 11, 1870. In June, 1861, General Sweeny took command of the Southwest expedition, and proceeded to Springfield, Mo., where he assumed command of all the United States forces in that part of the state, including Siegel’s and Saloman’s regiments, which had left St. Louis with two 4–gun batteries. July 20, General Sweeny took command of a flying column of twelve hundred men, moved on a depot of Confederate supplies at Forsyth, Mo., and captured the same. He led the Second Kansas regiment at the battle of Wilson’s Creek, Aug. 10, 1861, General Lyon leading the First Iowa. Sweeny was severely wounded, but after the death of Lyon favored following up the enemy. Sturgis, who succeeded Lyon in command, however, decided otherwise. As colonel of the Fifty-second Illinois, Sweeny was attached to General Grant’s army, and after the capture of Fort Donelson took charge of six thousand prisoners of war _en route_ to Alton, Ill. At the battle of Shiloh (Pittsburg Landing), April 6 and 7, 1862, Sweeny commanded the Third Brigade of the Second Division, Army of the Tennessee, the brigade comprising about five thousand, five hundred men. Towards the close of the first day’s battle, his command occupied a ravine near Gen. W. T. Sherman’s left, known as the “Hornet’s Nest.”