The Indiana Delta Chapter was chartered at Franklin College by David D. Banta in 1860. The college closed shortly after the Civil War because many students volunteered for the Union Army. In 1869, Franklin College reopened with William T. Stott as the president—the first Phi college president in history.

After graduation, William T. Stott, Franklin College 1861, served in the Union army for four years, fighting in fifteen battles and rising from private to captain at this time. After the war, he completed the Rochester Theological Seminary and served as a pastor before returning to his alma mater to be acting president. When the college reopened, two students happened to be former members of the Indiana Epsilon Chapter of Phi Delta Theta at Hanover College. With the help of David D. Banta and William T. Stott, these students revived the Franklin College chapter.