[7] On April 7, 1997, John Paul II appointed O'Brien as coadjutor archbishop for the Archdiocese of the Military Services, USA.

[8] From September 2005 to June 2006, O'Brien also served as the Vatican's coordinator for the papal visitation of seminaries and houses of priestly formation.

[10][11] His report also called for a stronger focus on moral theology, increased oversight of seminarians, and greater involvement of diocesan bishops in the formation process.

In 2006, O'Brien noted that declining public support for the Iraq War was leading to a decrease in morale among the troops, adding, "The news only shows cars being blown up, but the soldiers see hospitals being built and schools opening.

"[13] By 2007, he believed that the status of US operations in Iraq "compels an assessment of our current circumstances and the continuing obligation of the Church to provide a moral framework for public discussion.

[2] Recalling the call he received from the apostolic nunciature, O'Brien immediately accepted the appointment and later remarked, "I guess that's one thing I take from the military.

As head of the nation's oldest archdioceses, O'Brien held the status of primus inter pares in the American hierarchy.

Commenting on O'Brien's appointment, The Baltimore Sun said, "He has leapt from military airplanes, served in jungles during the Vietnam War and travelled extensively to current battle zones in Afghanistan and Iraq.

From his working-class roots ... to the upper echelons of Catholic power—carrying a Christian message of peace and love to some of the world's worst war-torn terrain".

"[20]On June 29, 2008, Benedict XVI invested O'Brien with the pallium, a vestment worn by metropolitan bishops, at St. Peter's Basilica in Rome.

[21] In October 2008, O'Brien dedicated the Pope John Paul II Prayer Garden in Baltimore, which he called a "sanctuary in a suffering city.

In March 2009, O'Brien said he was both "disappointed and bewildered" by the decision of the University of Notre Dame to have President Barack Obama deliver the commencement speech and receive an honorary degree at the university's graduation ceremony, given Obama's support for abortion rights for women and embryonic stem cell research (which the Church opposes).

[32] In 2008, O'Brien expressed his opposition to capital punishment, citing the John Paul II's encyclical Evangelium Vitae, although he had previously "thought it served a purpose.

[34][35][36] He condemned the Legion for its alleged practice of "blind allegiance",[34] lack of "respect for human dignity for each of its members",[35] and "heavily persuasive methods on young people, especially high schoolers, regarding vocations.

"[37] In June 2008, O'Brien called for greater "transparency and accountability" from the Legion and its lay arm, Regnum Christi, including both consecrated and non-consecrated members.

As a result, Martínez del Río directed the Legion and Regnum Christi chapters in the archdiocese to disclose all their activities to O'Brien.

"[36] O'Brien called Maciel "a man with an entrepreneurial genius who, by systematic deception and duplicity, used our faith to manipulate others for his own selfish ends.

[43][44] Early in 2003, O'Brien spoke at the United States Military Academy at West Point at mass: "I know that a lot of people have said that the Pope is against war with Iraq ...

[51] According to the journalist Sabrina Ferrisi, O'Brien's spiritual direction proved effective in calming the doubts of soldiers, advising them that they can safely leave the responsibility for moral decision-making to the US Government.

[54] O'Brien complained that too few Catholics priests were serving in active duty, being replaced by chaplains of other faiths because the military disregarded the significance of denominational affiliation.