On April 1, 1985, John Paul II appointed Egan as an
auxiliary bishop of New York He was
installed on December 14, 1988. During his tenure, Egan oversaw the reorganization of Catholic schools. He also raised $45 million for diocesan schools through a fundraising campaign, "Faith in the Future." The diocesan
Catholic Charities under his tenure became the largest private
social service agency in
Fairfield County, Connecticut. To support the 12
Hispanic parishes in the diocese, he brought
Spanish-speaking priests to Bridgeport from
Colombia. Egan also established a home for retired priests and a school for children with
special needs. Within the
United States Conference of Catholic Bishops (USCCB), Egan served as chair of the board of governors of the
Pontifical North American College and of the Committee on Science and Human Values. He was also a member of the Committee on Canonical Affairs, the Committee on Education, the Committee on National Collections, and the Committee on Nominations, and served two terms on the USCCB administrative board.
Archbishop of New York John Paul II appointed Egan as archbishop of New York on May 11, 2000, a week after Archbishop O'Connor's death. Egan was installed on June 19, 2000, with soprano
Renée Fleming performing at the ceremony. On becoming archbishop, Egan prioritized the encouragement of vocations to the priesthood. Besides private initiatives, each year on the
Feast of St. Joseph (March 19th), he offered a mass for prospective high school and college men. Egan appointed two priests as vocation directors to aid him in promoting the priesthood, although they were unable to reverse the declining trend. Egan was elevated to the
cardinalate by John Paul II at the
consistory of February 21, 2001, becoming the
cardinal-priest of the
Basilica of Ss. Ioannis et Pauli in Rome As cardinal, one of Egan's main concerns was the archdiocesan seminary in
Yonkers, New York. In March 2001, he announced the restructuring of the seminary faculty. A
Staten Island pastor, Reverend Peter Finn, was chosen as seminary rector. The minor seminary, then located in
Riverdale, Bronx, was moved to the campus of the major seminary. Egan was a prominent influence in New York City after the
September 11, 2001, attacks at the
World Trade Center in Manhattan. According to an article in
Catholic New York:In 2002, the
Institución del Mérito Humanitario in
Barcelona, Spain, awarded Egan the "
Gran Cruz al Mérito Humanitario". Also in 2002, John Paul II named Egan to the
Supreme Tribunal of the Apostolic Signature, the church's highest court of canon law. For retired priests, Egan established the John Cardinal O'Connor residence in 2003 at the previous site of the minor seminary in Riverdale. In 2003, Egan was accused of concealing the names of priests who had been
accused of child molestation, but found not guilty by the church. His spokesman argued that the innocent should be protected, while groups such as
Voice of the Faithful criticized the process as being out of the public view. Egan participated in the
2005 papal conclave in Rome that selected
Pope Benedict XVI. In 2006, Egan began hosting a weekly program on
The Catholic Channel of
Sirius Satellite Radio. He discussed events in the archdiocese and issues in the church. The channel also broadcast his Sunday mass from the cathedral. Egan in January 2007 announced the closure of ten under-utilized parishes and the merger of 11 other parishes. He stated that this was, "based on the migration of Catholics in the inner-city to the outer boroughs". He also announced the establishment of five new parishes; three in
Orange County. New York, one in
Staten Island and one in
Dutchess County, New York. Building projects were also approved for nine parishes. The closures caused some discontent among the affected parishes. On December 15, 2007, Egan celebrated his 50th anniversary as a priest.
Pope Benedict XVI appointed him to the
Congregation for the Oriental Churches on January 26, 2008. Egan then hosted the
papal visit to New York during April 2008, marking the 200th anniversary of the diocese. In 2009, Egan publicly condemned controversial statements made by
Richard Williamson, an
excommunicated Catholic bishop, about the reality of the
Holocaust. ==Resignation and final years==