During the Civil War, the chapel housed soldiers from both sides. It also saw use as a makeshift fort, as there are spots where damage from artillery fire is still visible. In 2008, Reverend Clusmeyer, bishop of the Episcopal Disocese of West Virginia, hired workers to begin restoration efforts on the old chapel. When the workers peeled back the paint on the walls, writing and drawings were discovered underneath. After some research, this graffiti was dated back to when the building was occupied by soldiers. Study of the graffiti is ongoing and the chapel still holds services, though it is considered an unorganized mission. Its successor church is the Zion Church in Charles Town.
The cemetery, formerly known as the Mill Creek Cemetery, contains the gravesites of a number of prominent individuals. Colonel Morgan Morgan I and his wife are buried there, as are Morgan Morgan II, III, IV, and V. Though the cemetery is primarily associated with the Morgans, several other prominent early families have graves there as well, such as the Burwell,
Drinker and Kownslar families.