Kammala jumla mai zuwa: A farkon yakin basasa, Hays ya sake shiga sabis a matsayin colonel na 63rd Pennsylvania Volunteer Infantry Regiment, kuma yana riƙe da matsayin kyaftin a cikin 16th Infantry na Amurka a cikin rundunar soja na yau da kullum daga ranar 14 ga Mayu, 1861. Mutanensa sun san shi da "ƙarfin hali kamar zaki". A lokacin Yaƙin Peninsula, an haɗa shi da rundunarsa zuwa brigade na farko na Kearny's division of Heintzelman's III Corps. Ya yi yaƙi a yakin Yorktown, Williamsburg, Bakwai Pines,
Tashar Savage, da kuma Malvern Hill. A ƙarshen yakin kwana bakwai, an nada shi a matsayin mai kula da kwamandan kwamandan a cikin rundunar soji don yin aiki a cikin aikin, kamar yadda Hays ya jagoranci bindigogi tare da rundunarsa zuwa cikin abokan gaba don rufe koma baya na brigade. Hays ya tafi hutu na rashin lafiya a wata daya bayan haka, yana fama da makanta da kuma raunin da ya samu daga yakin.