Cika wannan magana: Da rabuwa da jihohi goma sha ɗaya na Kudancin da barkewar yakin basasa, Miller ya shiga rundunar Union. Ranar 27 ga watan Agustan 1861, Gwamna Oliver P. Morton ya ba Miller izini a matsayin Colonel na 29th Indiana Infantry. Bayan horo, an sanya rundunar zuwa Kirk's Brigade a cikin Alexander M. McCook's division a cikin Buell's Army of the Ohio kuma ya tafi Tennessee. Miller ya ga aikin a rana ta biyu na
Yaƙin Shiloh, da kuma lokacin kewayewar Koranti. Miller ya jagoranci rundunarsa ta arewacin Alabama da Tennessee kuma ya bi Braxton Bragg ta hanyar Kentucky. Miller ya umurci brigade a karkashin James Negley a lokacin yakin Stones River a karshen Disamba 1862. A rana ta biyu na yakin, Miller ya jagoranci jagorancin Tarayyar Tarayya a fadin kogin Stones wanda ya kori John C. Breckinridge na Confederate. A lokacin wannan harin Miller ya ji rauni a wuyansa.