Impressed with the intelligence-gathering unpredictable nature of balloon flights, were possibilities of manned balloons, Abraham Lincoln appointed Thaddeus Lowe chief of army aeronautics in 1861; by the time he resigned his post in 1863, Lowe and his crew had made more than 3,000 flights over enemy territory.

A few months before he received his appointment, Lowe, a renowned aeronautic scientist, made a 9-hour, 900-mile flight from Cincinnati, Ohio to Unionville, South Carolina. Unfortunately, his trip followed the fall of Fort Sumter by just a week; when he arrived in South Carolina, the Confederate army summarily arrested him on charges of spying for the Union. Lowe managed to convince them of his innocence and took a week of touring through the Confederate states under a letter of free passage to Cincinnati where he was to recover his balloons. While in Cincinnati he received word to see the Secretary of the Treasury and the War Department. After which he was referred to the President and then eventually General Scott.

Working under the auspices of the War Department, Lowe received the pay of a colonel, plus materials and labor. His first mission involved gathering information on Confederate troop deployment shortly after First Bull Run in mid-July 1861. During George B. McClellan's Peninsula Campaign in the summer and fall of the same year, Lowe conducted almost daily flights over the Virginia landscape, producing reports and photographs of the Confederate position.

Thanks to additional army appropriations, Lowe was able to expand and improve his fleet. He built five airships of various sizes and had with them newly designed generators that could produce hydrogen gas on the battlefield. The largest of his ships, the Intrepid, was 32,000 cubic feet in size and required 1,200 yards of silk ' He used it to conduct surveillance during and after Fredericksburg.

Although the Confederate Army lacked the resources to launch its own full-scale aeronautics program, Captain E. Porter Alexander oversaw several ascensions by Confederate aeronauts in 1861 and 1862, who reported on Union troop deployment during the Peninsula and Seven Days campaigns. Balloons were often shot down behind enemy lines or, due to the unpredictable nature of balloon flights, were unable to return to camp in time to provide crucial information to the command. The last use of balloons by the Confederate army took place in 1863, after its largest balloon was swept away by a strong, high wind.

The Union soon abandoned the often risk use of surveillance balloons as well. Lowe ended his career with the Union army when the newly appointed commander, Joseph Hooker sharply reduced the role of aeronautics in the Army of the Potomac in late 1863. Shortly after the war ended, Lowe moved to California, where he continued experimenting with aeronautics and other new technologies. The Lowe Observatory in Pasadena, California, was built as a testament to his scientific accomplishments.