Following the battle, Slough received direct orders from Canby to remain at Fort Union. Though dated and sent before the battle, while the Confederate army divided Canby and Slough's communication line, the order has been debated as confirmation or not that Slough had disobeyed Canby's orders by leaving Fort Union in the first place. Slough met with Canby, determined the war in New Mexico was over, resigned his commission, and immediately headed to the Eastern theater. At the first anniversary after the battle of Glorieta, his former Colorado troops sent him a gold inlaid sword as thanks for making the rag tag volunteers into a fighting force. In response Slough wrote: “Remember the holy character of the cause in which you are engaged. Remember that you are American soldiers, battling in the cause of universal freedom.”