John McMillan was commissioned as Chaplain in the Union Army, 109th PA Infantry in May 1862. The 109th was formed in March 1862 and mustered in at Philadelphia later in the spring. It was engaged at Cedar Mountain, in which the unit suffered heavily, less than half of its number coming away unhurt. The unit missed Antietam, being on guard duty at the time, but were engaged at Winchester. They arrived too late to fight at Fredericksburg. They remained in the Eastern Theater, being engaged at Chancellorsville, after which they transferred Raccoon Mountain in Chattanooga, opposite Lookout Mountain. In winter 1864, most of the unit veteranized, and after their furloughs, joined Gen. Sherman on his march to Atlanta, and on to the sea. They mustered out in Washington in July 1865.

McMillan's first journal recounts how while he was in Manassas, Confederate forces attacked in force about midnight, and he and 80 armed men were forced to surrender. After some confusion about what to do with their prisoners, their captors marched them a couple miles south, where, he states, we were halted by order of Genl. “Stonewall” Jackson, marching back to Manassas. Toward evening, he was allowed to meet Genl. Taliaferro, who ordered the chaplain released. He was then introduced to Genl. A.P. Hill, who also ordered him to be “unconditionally released.” He could return to his regiment, on the condition that he give no information about the strength or position of the Confederate units. The generals, including Taliaferro and Jackson, also examined his diary, in part to satisfy themselves that he was indeed a chaplain. McMillan discusses trying to retrieve his diary from the generals, even stating his case to Jackson, who promptly said he had no desire at all to examine my private diary and said that Genl Taliaferro would be kind enough to return it to me. McMillan also noted, I must say that as men and as gentlemen I admire Genls Jackson and A.P. Hill – the latter was peculiarly courteous to me – so all of them were. He writes at some length about how not only the Generals, but all of the Confederates that he met were kind and courteous. When they were captured, they had no food other than a few crackers late in the day. It turned out that this was all the Confederates had to eat themselves, and they had shared what little they had with their prisoners. A mere 18 hours after his capture, he was free and began making his way toward Alexandria.