After little more than a decade of renewed enegy, Grace Church found itself in the midst of its third war — the War Between the States. Yorktown still being a strategic point, the town underwent two occupations during the war. The first, by Confederate troops, lasted through May 1862. During this period, the town was likely evacuated of much of its civilian population. Episcopal services may have continued, under the leadership of clergy or lay people. From time to time, troops like the Wythe Rifles, the Washington Artillery, and other Peninsula units were quartered in the church. "The large old horizontal gravestones in the churchyard served as mess tables...." [To the Gates of Richmond, Stephen W. Sears, 1992.]

During the long Union occupation, however, it appears that the church was closed as a church and may have seen service as a hospital. Following the end of the Peninsula campaign, it is likely that town life resumed some sort of normalcy. Virginia was readmitted to the Union on January 26, 1870. During the war, the Southern Episcopal churches formed their own national church. Prayer books of this period were written over in the South to omit offensive prayers for the President of the United States. The Southern dioceses were never stricken from the roll of the General Convention, however, and were welcomed back into the fold in 1865. [An Outline History of the Episcopal Church, the Rt. Rev. Frank E. Wilson, 1932]

Grace Church has no report listed in the 1865-1870 council records of the Diocese of Virginia — only name and location are given. In the early 1870's, reports of a stirring of parish life begin to appear. [Annuals of Council, Diocese of Southern Virginia]

Charlie Gilliam, a Grace Church parishioner, recalls a story of his grandfather, Richard Benjamin Gilliam, who was born in York County at the Halfway House, (near the "Cheesecake Church,") an inn halfway between Yorktown and Williamsburg: When the Civil War began, Ben was 14 years old and, anxious to do his part, he enlisted in the Confederate Army. When his age was discovered, he was sent back home, only to re-enlist when he was 17. While he was stationed at Gloucester, he missed his sweetheart back home so much that he decided to swim his horse across the York River to see her. Exhausted by the swim, and arriving so late, he sought refuge in York-Hampton Church for the rest of the night. After seeing to his horse, he entered the church and collapsed on the floor, fast asleep. Not long afterward, some townspeople came into the church and began to pray. So fervent were their prayers as they called on the Lord for help, that they soon awakened Ben, whereupon he called out, "Who's there, and what do you want?" This unexpected quick response to their prayers, coming right out of the dark, was too much for the petitioners, and they bolted out of the church and ran away.

After a nearly 15-year silence, Grace Church is again heard from, beginning in the record of diocesan council for 1875. The Rev. Dr. L. B. Wharton, a professor at the College of William and Mary, reports to the bishop in that year: "In addition to my College duties, I have officiated once a month at Yorktown, where we have 7 communicants ... we are endeavoring to finish the repairs on the Old Parish Church of York-Hampton Parish, which the war left entirely unfit for use."

Wharton ministered faithfully without pay to the people of Grace Church for more than 20 years. In 1894, the Rev. William Byrd Lee mentions in his report to annual council that Wharton, "as a work of love," is still assisting with services at Grace once a month. Wharton died in 1907, on his way to a Confederate reunion in Richmond; his obituary tells that he dropped dead in the Williamsburg train station, just in the act of buying a ticket — "His reunion was with the greater hosts of the dead."

From 1878 to 1883, Wharton was supplemented by the Rev. Alexander Hundley of Gloucester. Hundley began his ministry at Grace while still a deacon.

In addition to these long-term missionaries, Grace Church was tended from time to time by the clergy of Bruton Parish in Williamsburg and Abingdon and Ware parishes in Gloucester County.

In his 1879 report to the diocesan council, the Rev. Alexander Hundley writes "I wish it to be recorded, that although living in Gloucester country and separated from the church in Yorktown by the York river, yet I have never, since taking charge of the Parish, failed to meet a single appointment on account of not being able to cross the river."

TimeLine of Significant Events

• 1861 - Beginning of the Civil War
• 1862 - Southern Bishops form Confederate Episcopal Church
• 1863 - Emancipation Proclamation
• 1865 - Civil War ends; Southern Bishops rejoin Episcopal Church
• 1870 - Grace Church reappears in the diocesan records
• 1878 - From annual report to the diocese, "total (white) communicants: 16"
• 1881 - Yorktown Victory Monument dedicated at centennial observance of cornwallis' surrender
• 1882 - Parish's ancient bell, broken in 1860's and lost, is recovered and recast