Armed with equal education ideals, he believed that the blind should no longer be doomed to inequality, to becoming only "mere objects of pity." During his first years as director [of the Perkins Institution for the Blind], he visited seventeen states, establishing schools in Ohio, Tennessee, Kentucky, and Virginia. He also developed an embossed-letter system for the blind to read, first known as Howe Type, and later as Boston Line Type. It was used at Perkins until Braille came into common usage at the turn of the century.

Strongly attached to his native state and convinced that civil war was inevitable, Hill resigned from the army on 1 March 1861 to await Virginia's call. It soon came with the colonelcy of the Thirteenth Virginia Infantry Regiment. From the moment he entered Confederate service, "Little Powell" was a familiar figure. He stood five feet, nine inches tall but weighed only 145 pounds. His chestnut hair was wavy and worn long. Catching immediate attention were his hazel eyes, which stared intently and assumed a steely glint in anger or in battle. Hill disdained uniforms and ornaments.

A first lieutenant when the Civil War erupted in 1861, Howard became colonel of the Third Maine, a volunteer regiment. In command of a brigade at Bull Run (Manassas) in July, he was promoted to brigadier general two months later. The next spring his right arm was badly shot up at Fair Oaks, and most of it had to be amputated. Howard returned to service in August 1862 and commanded troops at Antietam and Fredericksburg.