Despite the loss of an arm, he returned to the Army and was present at the battles of Champion Hill, Big Black River Bridge, and in the siege of Vicksburg. Always the geologist, he took to studying rocks while in the trenches at Vicksburg. He was made a major and commanded an artillery brigade with the 17th Army Corps during the Atlanta campaign. After the fall of Atlanta he was transferred to George H. Thomas’ army and participated in the battle of Nashville. At the end of the war he was made a brevet lieutenant colonel but preferred to use the title of “major”.