O'Brien was Apostolic Administrator of the Diocese of Argyll and the Isles from 1996 until 1999, when Bishop Ian Murray took over the diocese. O'Brien took part in the 2005 Papal Conclave which elected Pope Benedict XVI. In anticipation of the 2010 visit of Pope Benedict to England and Scotland, O'Brien and Vincent Nichols, Archbishop of Westminster, said that the crisis involving Seán Brady, Archbishop of Armagh, over the priest Brendan Smyth and other clerical abuse charges was one for the Irish Catholic Church and should not overshadow Benedict's visit. O'Brien and Nichols were asked whether the pope would respond to charges made against the church about clerical sex abuse during his four-day visit, the first papal visit to the UK since John Paul II in 1982. O'Brien said he did not know; Nichols said English, Welsh and Scottish bishops had "robust" rules in place to protect children. Campaigners for victims of abuse wanted an investigation of the way O'Brien dealt with all allegations of abuse while he was leader due to O'Brien's sexual misconduct admission. Mario Conti, Archbishop emeritus of Glasgow, said all the Scottish Catholic bishops except O'Brien cooperated over an independent inquiry into the handling of child abuse in Scotland between 1952 and 2012 with the results to be published. The inquiry was delayed because O'Brien and only O'Brien withdrew cooperation.