Tuhia he tohutoro mō tēnei wāhanga - I te tīmatanga o te Pakanga ā-Iwi o Amerika i te tau 1861, ka tono a Jones kia uru ki te ope taua o te Kotahitanga. I te Oketopa 3 i pootihia ia hei rangatira mo te 53rd Ohio Infantry Regiment, a i kite ia i nga mahi penei i te Pakanga o Shiloh me te Siege o Koriniti. I te Mei 2, 1862, ka riro a Jones hei koroneela o te 53 o Ohio me tana rangatira rangatira. I arahina e ia tana rerenga i te whakapae o Vicksburg me te pakanga o Missionary Ridge, i te tau 1863. I kite a Jones i etahi atu mahi i roto i te 1864 Atlanta Campaign, e whawhai ana i Resaca, Dallas, Kennesaw Mountain me Atlanta
He aha? I te marama o Akuhata, i tohua a Jones hei rangatira pirihimana i te wa i whara ai tana rangatira rangatira, a Brigadier General Joseph A. J. Lightburn, ka whakarere i te whakahau mo te toenga o te pakanga. Ko Colonel Jones inaianei i arahi i te 2nd Brigade i te Wahanga 2 o William B. Hazen o te XV Corps i Jonesboro. He mea tupono, ko te 1st Brigade o taua wehenga i arahina e tetahi atu "Colonel Jones", Theodore Jones o te 30 o Ohio. I uru a Wells Jones ki te 1864 Maehe ki te Moana, a i whara ia i nga mahi huri noa i Fort McAllister, Georgia, i te Tihema 13.