Cardinal Desmond Connell, who retired as the Roman Catholic archbishop of Dublin during a furor over the church’s handling of cases of sexual abuse perpetrated by members of the clergy, died Tuesday. He was 90. The death, in Dublin, was announced by the current archbishop, Diarmuid Martin. A theological scholar with training in metaphysics, then-Father Connell was a surprise choice when Pope John Paul II appointed him to lead the archdiocese of Dublin in 1988. John Paul named him a cardinal in 2001, making him the first archbishop of Dublin to be so elevated in nearly 120 years. During his 16 years as archbishop, he was a stalwart defender of church doctrine, particularly on social issues such as contraception, divorce and homosexuality. At times he came across as too doctrinaire. He criticized Mary McAleese, a Roman Catholic who was president of Ireland from 1997 to 2011, for taking Communion in a Protestant church. At an awkward reception hosted by Bertie Ahern, the prime minister at the time, and his partner (the two were not married), the cardinal spoke of the primacy of marriage and the family. Archbishop Connell used his pulpit to reduce archdiocesan debt, to speak out on issues such as unemployment and to defend the treatment of the Irish Travellers, a nomadic minority that has historically been stigmatized. He was one of the earliest and most senior prelates in Ireland to express concern about the treatment of refugees and asylum seekers. But he was best known for his handling of a sex-abuse scandal that eventually engulfed his archdiocese, as it has others around the world. The abuses began to emerge after Rev. Brendan Smyth, a Northern Irish priest, was convicted of child sex abuse and imprisoned in 1994. The next year, the archbishop denied that the archdiocese had paid compensation to victims of abuse by its priests. But in 1998, it came to light that he had quietly lent archdiocesan money to an abusive priest, Rev. Ivan Payne, who then paid an abuse survivor, Andrew Madden. Mr. Madden came forward to reveal the loan, but Archbishop Connell initially denied that he had made it. In the ensuing controversy, he was accused of participating in a cover-up. In 2002, the national broadcaster RTE published a report by investigative journalist Mary Raftery exposing the archdiocese’s protection of eight priests who had sexually abused children. An independent commission was established to investigate the archdiocese’s handling of 325 abuse claims from January, 1975, to May, 2004. But Cardinal Connell mounted a High Court challenge to try to block the inquiry from gaining access to 5,500 files on priests and abuse allegations. He secured a temporary injunction, before withdrawing his action two weeks later amid public outrage. The inquiry, led by Judge Yvonne Murphy, issued a damning conclusion in 2009. “The Dublin Archdiocese’s preoccupations in dealing with cases of child sexual abuse, at least until the mid-1990s, were the maintenance of secrecy, the avoidance of scandal, the protection of the reputation of the church and the preservation of its assets,” the commission found. “All other considerations, including the welfare of children and justice for victims, were subordinated to these priorities.” Cardinal Connell, the report found, had been “personally appalled by the abuse,” but it had taken him “some time to realize that it could not be dealt with by keeping it secret and protecting priests from the normal civil processes.” His critics said Cardinal Connell had a talent for equivocation. For example, he initially denied using diocesan funds to compensate victims – but later said he had used the present tense to say that payments were not being made at that moment. He had not said that payments had not been made in the past. Desmond Connell was born in Dublin on March 24, 1926, the son of a civil servant. He was educated by the Jesuits at Belvedere College in Dublin and attended Clonliffe College, Dublin’s diocesan seminary. Ordained in 1951, he went on to earn a doctorate in philosophy at University College, Dublin. He later became a professor of general metaphysics and dean of the philosophy faculty there before he was appointed archbishop. He leaves three nephews.