Rubuta ci gaba ga wannan sakin layi - Bayan barkewar yakin basasar Amurka, Jones ya shiga rundunar Union. A ranar 7 ga Yuli, 1861, ya shiga cikin 37th New York Volunteers, wanda aka fi sani da "Irish Rifles", a karkashin Kanar John H. McCunn. Da farko ya kasance mai zaman kansa amma da sauri ya sami kansa a zaɓa shi a matsayin na biyu a cikin maza a cikin rukunin. Ya kasance a lokacin yakin farko na Bull Run, makonni biyu kawai bayan da ya shiga, amma bai ga wani aiki ba yayin da aka gudanar da ajiyar. Jones ya nuna "halayyar kirki" a lokacin da yake farkon shekaru tare da rundunar kuma ba da daɗewa ba ya tashi a matsayin mai ba da shawara na farko da mai ba da shawara a ranar 4 ga Nuwamba, 1861, sa'an nan kuma manyan a ranar 21 ga Janairu, 1862. Shi da "Irish Rifles" daga baya suka shiga Janar Samuel P. Heintzelman's III Corps, a matsayin wani ɓangare na Brigade na 3 na Division na 3 karkashin Brigadier Janar Philip Kearny, a lokacin yakin Peninsula kuma ya shiga Williamsburg, Bakwai Pines
da kuma yakin kwana bakwai. Jones ya kasance a lokacin da 37th New York Volunteers, sa'an nan kuma a haɗe da 3rd Brigade na 1st Division na III Corps, sun kasance a karo na biyu na Bull Run. A watan Mayu da Yuni, ya fara fama da zazzabin cizon sauro kuma an kwantar da shi a asibiti a Washington, D.C. a ranar 26 ga Satumba inda ya kasance har zuwa karshen Oktoba. Ya kuma kasance ɗan gajeren lokaci ga Manjo Janar Franz Sigel kafin janyewar Janar Ambrose Burnside da sake fasalin Sojojin Potomac.