Wheeling was in an untenable position when the Virginia Assembly voted to secede from the Union in April 1861. Wheeling, more north than Philadelphia, and with the free states of Ohio and Pennsylvania at either side, was thrown into turmoil. While Confederate troops were mustered out in Wheeling, it was really the Unionist cause that fired the populace. The rhetoric was fierce and the war raised the level of hostility among neighbors. John Mitchell informed the governor that secessionists in Wheeling "might grace a lamp post at any time." Episcopalians with their Richmond, Va., connections were suspect. It's no wonder that Rev. E. T. Perkins suddenly abandoned the rectory by night, leaving even his household goods, to take his family to the security of Richmond. Later, he agreed to return to Wheeling if the Vestry would permit him to omit the prayers for the President of the United States in the liturgy. The Vestry declined and engaged The Reverend Thomas G. Addison who believed that the president did, indeed, need the prayers of the church.
Aside from the hostility and fear that gripped Wheeling, St. Matthew's and the other churches in western Virginia found themselves suddenly cut off from their bishop. Bishop Johns rather quickly led the diocese out of the Protestant Episcopal Church of the United States into the newly formed Protestant Episcopal Church of the Confederate States of America, meeting in Columbia, S. C., in October 1861. Many in western Virginia churches were irate as a letter in the St. John's Vestry minutes to The Reverend George Jenks relates:
"You are aware that the Bishops of Virginia have participated in the schismatic action of the Southern Bishops, and otherwise manifested their disloyalty to both church and state. So long as they advocate treason and schism, the loyal people of western Virginia can have no connection or intercourse with them. We are consequently deprived of all Episcopal services or aid, and cannot expect to have the benefits of either until relieved by the General Convention. We trust however that you will not be deterred by this unhappy condition of the church in this part of Virginia from accepting the charge we tender you."
The St. John's Vestry ordered "the wardens and registrar to secure a national flag and cause it to be placed on the tower of the church.
St. Matthew's shared the same situation although the Vestry correspondence was more restrained. Rev. Mr. Addison was asked to write to Bishop Johns for permission to seek Episcopal services elsewhere. He wrote:
"My dear Bishop It is very important to the interest of St. Matthew's Parish that we should have an Episcopal Visitation, an inasmuch as you, our own beloved Bishop, are kept from us, and may be kept from us for years by the war, we are constrained to beg that you will give your consent to our inviting a Bishop to officiate in your stead. Will you not give us a discretionary power as to the selection of a Bishop? Affectionately, your humble servant, Thos. G. Addison."
The bishop responded that he'd certainly make a visit, it being three years since his last, if Rev. Mr. Addison would not only supply him with safe conduct, the conditions of which "will be sacredly observed by me," but also with the distinct understanding that such conditions "are not in conflict with my obligations to the government under which I live." Otherwise he knew that it was not his fault that he had deprived services to a portion of his cure. It is recorded that the Right Reverend G. T. Bedell, bishop of Ohio, made several visits to Wheeling. He always required the Vestry to put the request in writing and, in at least one instance, asked them to include his response on their minutes. This is his letter to the St. John's Vestry after assisting them in the call of a new rector:
"The circumstances of the case are so peculiar that I beg to be distinctly understood as not claiming any right under the canons to authorize The Reverend Mr. Jenks to officiate in Virginia. The exigency (for which no canon could have provided) seems to create a necessity. Do me the favor of recording this statement upon the books of your Vestry, at your next meeting. Prayer for Divine blessing on the labors of my friend and brother in your midst, I am sincerely your G. T. Bedell."
Interestingly, when the war was over, the bishops quietly returned from the Protestant Episcopal Church of the Confederate States of America, to the General Convention of the Protestant Episcopal Church of the United States without fanfare or recrimination.