On June 11, 1851, Sweeny was promoted to be first lieutenant in the Second Infantry. In 1852 he engaged in the Yuma Indian War, and commanded an expedition of twenty-seven men, who penetrated into the Cocopa country in May, and after a sharp engagement, captured one hundred and twenty-five armed warriors and marched them into Camp Yuma, where a treaty was entered into which broke up the confederation of the River tribes. While engaged on this duty, Sweeny received a severe arrow wound in the neck.
In 1854 he was ordered to Fort Pierre, in what was then northern Nebraska, where he served as aid to Gen. William S. Harney, participating in the campaign against the Sioux in 1855–’56, and was present at the “Great Treaty” made with the Sioux nation at Fort Pierre, at which many famous chiefs were present. In 1858 Sweeny was ordered to New York city on recruiting service, and was stationed there when the Rebellion broke out.
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.”
Speaking of this battle General Sherman has said: “I remember well that Col. Thomas W. Sweeny, a one-armed officer who had lost an arm in the Mexican war and did not belong to my command, stood near by and quickly spoke up: ‘I understand perfectly what you want; let me do it.’ ‘Certainly,’ said I; ‘Sweeny, go at once and occupy that ravine, converting it into a regular bastion.’ He did it, and I attach more importance to that event than to any of the hundred achievements which I have since heard ‘saved the day,’ for we held that line and ravine all night, and the next morning advanced from there to certain victory.”
In this battle Sweeny was again wounded, “receiving a minié ball in his remaining arm and another shot in his foot, while his horse fell riddled with seven balls. Almost fainting from loss of blood, he was lifted upon another horse and remained on the field through the entire day. His coolness and his marvelous escapes were talked of before many campfires throughout the army.”
Capt. C. H. Fish, Fifty-second Illinois, speaking of the first day’s battle at Shiloh, wrote of Sweeny: “Colonel Sweeny came riding up the line and reached our regiment, but not recognizing it, asked: ‘What regiment is this?’ On my telling him it was the Fifty-second Illinois, he said: ‘Well, I am at home once more. I guess I will stay here.’ Our colonel had only one arm—the left one; the other he lost in Mexico. When on drill or review he held the reins in his teeth and sword in left hand. The balls seemed to fill the air at this moment, the firing was so terrific, but our colonel [Sweeny] coolly sat on his horse, quietly smoking a cigar, ever and anon removing it and puffing forth vast quantities of smoke. Presently a minié ball came cutting through the air, struck his cigar, and cut it off at his teeth, doing some slight injury to his moustache. Yet not a muscle moved. He quietly replaced the cigar with a fresh one and smoked away.”
After the battle of Shiloh, Sweeny was granted a leave of absence owing to disability resulting from wounds received. During this period he was presented an elegant sword by the city of Brooklyn, N. Y. At the expiration of his leave, he again took the field, returning in time to participate in the battle of Iuka and the siege of Corinth—Oct. 3 and 4, 1862,—where he was again wounded, and had a horse shot under him. Gen. Thomas A. Davies, commanding the Second Division, in his report of the battle of Corinth, states that “Colonel Sweeny, commanding First Brigade, behaved in the most gallant manner throughout, and should be immediately promoted.”