Returning to the United States, Whelen became a faculty member and business manager at Mount St. Mary's, and also served as pastor of Harper's Ferry. His pastoral responsibilities included missions at Martinsburg, Winchester and Bath as well as numerous Catholic families who could not access Catholic institutions of any kind. On December 19, 1840, Whelan was appointed the second Bishop of Richmond, Virginia, by Pope Gregory XVI. He received his episcopal consecration on March 21, 1841 from Archbishop Samuel Eccleston, P.S.S., with Bishops Benedict Joseph Fenwick, S.J., and John Joseph Hughes serving as co-consecrators, at Baltimore. The second Catholic bishop in the United States, Bishop Jean Dubois had similarly initially lived in Richmond, but soon moved the seat of his extremely large diocese west to serve Catholics in remote mountain areas, as well as to escape anti-Catholic and other civil strife in Virginia's capitol. Furthermore, after the brief American episcopate of his predecessor, the seat had been vacant for more than a decade before Whelan's appointment and consecration, and Richmond had become a stronghold of the Know-Nothingpolitical party, known for its anti-Catholic and racial prejudices and propensity for mob violence. Since there were only six priests in the still very large diocese of Virginia at this time, Whelan appealed to the Societies for the Propagation of the Faith in Paris, Lyon and Vienna to increase the diocese's clerical ranks. He also established a seminary college on the outskirts of Richmond, where Whelan himself resided and taught when he was not visiting remote areas of the diocese. He also established several parishes, missions and schools. By 1848 Whelan requested that his see be divided, with the Allegheny Mountains as the natural boundary. The Holy See granted his request by creating the Diocese of Wheeling on July 19, 1850. Four days later, on July 23, Whelan was named Ordinary of the new Wheeling Diocese, and John McGill, a former lawyer, succeeded him as Bishop of Richmond. Bishop Whelan became a civic leader in Wheeling, the new diocese's largest city. It had grown because of its location on the National Road and access to both water and coal power. The Baltimore and Ohio Railroad formally reached Wheeling in 1853, but many Irish emigrants building that and other railroads or working in the new factories had already passed through or settled in the city. Other industrializing areas of the new diocese included Charlestown and to a lesser extent Huntington and Martinsburg/Berkeley Springs/Harper's Ferry. The mountainous new diocese consisted of several distinct valleys, with many immigrants but limited funds and access to social services. The new bishop became known for his resourcefulness, even performing carpentry and stone work himself. Bishop Whelan also did not escape anti-Catholicism or the Know-Nothings, for when a papal nuncio arrived on the new railroad in 1853, Catholics were instructed to stand guard in a ring around the Cathedral block to ensure the envoy's safety. When Virginia seceded from the United States in 1861 a Unionist government was organized in Wheeling, which chose as its governor Francis H. Pierpont. Bishop Whelan believed this government to be usurped and that the government in Richmond was the only state government. He refused to take the oath of loyalty, which included an oath to the Pierpont government, and was apprehensive about his probable arrest. President Lincoln learned of the intention to arrest the Bishop but the authorities in Wheeling were instructed on May 21, 1862, by Edwin M. Stanton- "The President being informed that you intend or threaten to arrest Bishop Whelan, the Catholic Bishop of your city, he directs that you take no action against the Bishop without the President's order." No actions were taken against Bishop Whelan during the course of the war. As in Richmond, Bishop Whelan invited religious congregations to his new diocese to provide needed social services. By the time he died, the diocese had 48 churches, 29 priests, three religious congregations of women, six schools for girls, a school for boys, an orphanage, and a hospital. From 1869 to 1870, Bishop Whelan attended the First Vatican Council, where he opposed papal infallibility because he thought such a declaration would be untimely.
Death and legacy
Bishop Whelan fell ill in 1874 and was taken to St. Agnes Hospital in Baltimore, where he later died from liver disease at age 65. A hall at Wheeling Jesuit University, the youngest of the nation's Jesuit Universities, is named for the pioneering bishop.
