When the Great Fire of 1860 turned most of Danville into ash, the Episcopal Church also was destroyed. The interior was burned to cinders and only the exterior walls were left standing. The congregation rallied, and within two years the church was repaired.
Residents marveled at the restored interior, which included two aisles (a middle section of pews and side pews), a pulpit, an anteroom, walnut woodwork and an organ. Danville housekeeper Mary E. Haffis noted that, "It was a very nice brick building, not very large, with stained glass windows. Very nicely carpeted with a yarn carpet. It had just one story, with (a) gallery at one end of it, and a small room-vestry room-at the rear. It had oak furniture, the pews (were naturally finished) oak. It was a comparatively newly finished church, because it had been bumed - two years before, I think. There was a small organ. There were chancel railing and desks and (a) table of oak. There were plain plastered walls."
Druggist H. E. Samuel concurred: "It was not a specially large church but it was a beautiful church - well finished inside. It had a tower or belfry on it and had a very nice gallery. It is my recollection (that) the pews were of oak and were cushioned. It was very comfortable." Local teacher Henrietta Wilson remarked that it was "A perfectly new church; just had been rebuilt after the fire; carpet new and fresh; furniture all new."
The aftermath of the Oct. 8, 1862, Battle of Perxyville ruined this "perfectly new" structure. As soon as the fighting ended, wounded and sick soldiers were placed in public and private buildings across the region. More than 3,000 sick Federal soldiers were placed in Danville, doubling the city's population. According to witnesses, wounded and sick Union and Confederate soldiers were placed in the Episcopal Church, and the occupation was a shock to the congregation. Mrs. H.L. Newlin, a Danville milliner, stated that members had "just began to get it ready to worship in (after the fire). I know some of the members were dreadfully distressed to think their church was being used for a hospital when they just had gotten it fixed up."
The occupation of Trinity Episcopal surprised many residents. "The first thing I knew of it was soldiers sitting in the door," stated local tailor Abraham Baker, "and the door was open, and I asked if the Episcopal Church had been taken as a hospital, and they said it had."
This is how most citizens discovered that the church had been occupied. Patty Bell Engleman said, "I could see the soldiers in the yard - there is a little yard in front - and I would see them in the yard, going in and out of the church, as if they were at home - as if they were occupying it."
By the end of October, the United States Sanitary Commission, an organization much like the modern Red Cross, brought supplies to Danville. At this point, nearly one month after the Battle of Perryville, there were still more than 1,400 sick troops in town. Dr. A.N. Read of the Sanitary Commission reported that 161 patients were crammed into the Episcopal Church. Read remarked that some of those soldiers slept inside, others slept in private homes, and some slept "out on the ground, no bedding or change of clothing. Cooking (was) done in one large and two small pots, and three frying pans."
Conditions were unsanitary and deaths were frequent. Mary Harris, who took provisions to many of the town hospitals (including the Baptist Church and the Danville Theological Seminary), said that "The first death I saw was a Federal soldier in the Episcopal Church."