In the spring of 1860, on a lecturing tour, he visited some of the Southern States, and while there closely observed the sentiment of the people on the subject of slavery, with the result that he expressed the conviction that nothing short of war could settle the matter. In the summer of 1860 he became principal of the public schools of Hennepin, Illinois. These he organised, graded, and taught with a vigour which was characteristic, yet never forgetting his geological investigations in the neighbouring country, where, on Saturdays and at other times when the schools were not in session, he made botanical and zoological collections.
Convinced that war was inevitable, the winter of 1860-61 found him studying military tactics and engineering. When the call came for troops, he was the first man to enroll, and largely through his efforts Company H of the 20th Regiment, Illinois Infantry, was raised in Putnam County. When the regiment was organised at Joliet, Illinois, he was appointed sergeant-major, and in this capacity went to the front. When the force was sent to Cape Girardeau, Missouri, his prescience in studying military engineering made him invaluable. He was practically given charge of planning and laying out and constructing the fortifications at that place, a work he executed so well that it received the unqualified commendation of General Frémont. The second lieutenant of Company H resigning, Powell was elected to fill the vacancy. After a service of a few weeks with his company he was put in charge of the fortifications he had constructed, being retained in this post after the departure of his regiment. In the early winter of 1861-62 he recruited a company of artillery, largely from loyal Missourians. This company was mustered into service as Battery F, 2d Illinois Artillery, John Wesley Powell, Captain. After drilling a few weeks he was ordered to proceed with his battery to Pittsburg Landing, Tennessee, where he arrived the latter part of March, 1862. The battery took part in the battle of Shiloh, April 6th of that year, and during the engagement, as Powell raised his arm, a signal to fire, a rifle ball struck his hand at the wrist glancing toward the elbow. The necessary surgery was done so hastily that later a second operation was imperative, which left him with a mere stump below the elbow-joint. Never for long at a time afterward was he free from pain and only a few years ago a third operation was performed which brought relief.