Shortly afterward, the 12th Illinois was ordered to Cairo, Illinois, and that September, it was part of the force used by Grant in the expedition against and capture of Paducah. Chetlain was then given command of Smithland, Kentucky, where he constructed fortifications to defend part of the Cumberland River. In January 1862, he rejoined his regiment, led it during the expedition up the Tennessee River, was at the capture of Fort Henry on February 6, and led his command during the Battle of Fort Donelson from February 12 to 16.