The fight over contraception and health-care reform was portrayed as various kinds of wars—on women, on religion, between the G.O.P. and Obama—but it also included a skirmish in a longer fight within Catholicism, with the Vatican and bishops on one side and American nuns on the other. On Wednesday, the Congregation of the Doctrine of the Faith, which for a few years has been conducting an inquiry into the Leadership Conference of Women Religious, the main association of American nuns—provoked, it said, by its discernment of “radical feminist themes” in the L.C.W.R.’s work—released a Doctrinal Assessment that found the L.C.W.R.’s state to be “grave and a matter of serious concern.” The nuns in question, according to the Vatican, “perpetuate a distorted ecclesiological vision, and have scant regard for the role of the Magisterium as the guarantor of the authentic interpretation of the Church’s Faith.” An archbishop and two bishops were being urgently dispatched to show them the error of their ways.

What have the nuns done that is so bad? The Assessment mentioned public statements “that disagree with or challenge positions taken by the Bishops.” The health-care debate might be an example. Sister Carol Keehan, the head of the Catholic Health Association and its six hundred hospitals—she received the L.C.W.R.’s Outstanding Leadership Award last year—had endorsed the Affordable Care Act when it was before Congress; President Obama gave her one of the pens he used to sign it. However, when rules requiring Catholic hospitals and universities to get their employees insurance that covered contraception were issued, this winter, Keehan, like the United States Conference of Catholic Bishops, objected strongly. The divergence came when the Administration offered a compromise. Sister Carol said that it worked for her. The bishops disagreed. Cardinal Dolan, of New York, told reporters that Sister Carol had “disappointed” him.

What is striking, though, is the absence of a smoking gun in the Congregation of the Defense of the Faith’s findings on matters of faith, other than faith in bishops (which is presented as one of the Church’s doctrines). What seemed to bother the Vatican’s investigators was not that nuns were speaking out on political matters, but that they were failing to engage politically in the way the Church wanted them to: the L.C.W.R. had been

silent on the right to life from conception to natural death, a question that is part of the lively public debate about abortion and euthanasia in the United States. Further, issues of crucial importance to the life of Church and society, such as the Church’s Biblical view of family life and human sexuality, are not part of the LCWR agenda in a way that promotes Church teaching.

The Congregation also noted

the absence of initiatives by the LCWR aimed at promoting the reception of the Church’s teaching, especially on difficult issues such as Pope John Paul II’s Apostolic Letter Ordinatio sacerdotalis and Church teaching about homosexuality.

In other words, instead of just talking about “social justice,” the nuns should be out on the barricades, agitating against abortion and gay marriage. And, again, they need to listen to the bishops.

What would this look like? In 2009, a woman arrived in the emergency room at St. Joseph’s hospital in Phoenix. She was twenty-seven years old, eleven weeks pregnant, and she was dying. Her heart was failing, and her doctors agreed that the only way to save her life was to end her pregnancy, and that her condition was too critical to move her to another, non-Catholic hospital. The member of the ethics committee who was on call was Sister Margaret McBride. She gave her approval, under the theory that termination of the pregnancy would be the result but not the purpose of the procedure. The woman, who had four small children, went home to them. When the Bishop Thomas Olmsted of Phoenix heard what happened, he excommunicated Sister Margaret on the spot. A Church that had been so protective of priests who deliberately hurt children—keeping them in its fold, sending them, as priests, to new assignments—couldn’t tolerate her. A spokesman for the diocese called her a party to “murder.” (Sister Carol, speaking for the C.H.A., expressed support for what she had done in a “heartbreaking situation.”) Sister Margaret was able to take communion again after she repented. The hospital and the Church ultimately ended their affiliation.

The Congregation of the Doctrine of the Faith has now named the Archbishop of Seattle as its Delegate, with a five-year mission to rewrite the L.C.W.R.’s bylaws and redirect its statements and actions. Sister Annmarie Sanders, the director of communications for the conference, said in a statement that “we were taken by surprise” and “stunned by the conclusions” by the assessment. She added, “We ask your prayers as we meet with the LCWR National Board within the coming month to review the mandate and prepare a response.”

Photograph of Sister Carol Keehan by Brendan Smialowski/The New York Times/Redux.