In the beginning, there was the Conference of Major Religious Superiors of Women's Institutes, which was established with the Vatican's blessing in 1959 during an era of rapid growth for Catholic religious orders.

Then along came two cultural earthquakes: the Second Vatican Council and the Sexual Revolution. In 1971, the women's conference changed its name -- this time without the Vatican's blessing -- to become the Leadership Conference of Women Religious. Two leaders in this transformation later wrote that the goal was to become a "corporate force for systematic change in Church and society."

The rest is a long story, ultimately leading to a blunt April 18 missive from the Congregation for the Doctrine of the Faith. This long-expected Vatican broadside noted "serious doctrinal problems" in LCWR proclamations, characterized by a "diminution of the fundamental Christological center" and the prevalence of "radical feminist themes incompatible with the Catholic faith."

Women's conference leaders offered a terse response, saying they were "stunned by the conclusions of the doctrinal assessment" from Rome.

"Stunned" was the key word for legions of headline writers, whose work resembled this Washington Post offering: "American nuns stunned by Vatican accusation of 'radical feminism,' crackdown." The Chicago Sun-Times went even further, proclaiming: "Vatican waging a war on nuns."

Truth is, tensions have been building for decades between the LCWR leadership and Vatican leaders. Thus, the Congregation for the Doctrine of the Faith missive stressed that its call for reform was built on a lengthy study of materials created by "a particular conference of major superiors and therefore does not intend to offer judgment on the faith and life of Women Religious in the member congregations."

This particular investigation began in 2008 and Catholic leaders first discussed some of its findings two years later. The final "doctrinal assessment" document was completed in January of 2011. Some of the specific events criticized in the Vatican document took place during the 1970s and '80s.

It "certainly didn't help matters" that there has been so much publicity about liberal nuns supporting White House health-care policies and new Health and Human Services regulations that require most religious institutions to include free coverage of all FDA-approved contraceptives in their health-insurance plans, noted John L. Allen Jr. of the National Catholic Reporter.

Nevertheless, "it doesn't withstand scrutiny for anyone to say that this conflict is about the bishops and Rome being upset about the sisters, Obama and birth control," said Allen in a telephone interview from Rome. Also, "no one is upset about all the sisters have done to abolish the death penalty, stand up for immigrants, care for the sick and help the poor. Rome praised them for that. ...

"Frankly, this report could have been written 20 years ago. The real issues in this case are that old."

For example, the Vatican noted that in 1977 the LCWR leadership openly rejected Catholic teachings on the "reservation of priestly ordination to men." The women's conference later published a training book suggesting that it's legitimate for sisters to debate whether celebrations of the Mass should be central to events in their communities, since this would require the presence of a male priest. In the '80s, leaders in female orders backed the New Ways Ministry's work to oppose Catholic teachings on homosexuality.

A pivotal moment came in 2007, when Dominican Sister Laurie Brink delivered the keynote address at a national LCWR assembly stating that it was time for some religious orders to enter an era of "sojourning" that would require "moving beyond the church, even beyond Jesus."

With the emergence of the women's movement and related forms of spirituality, many sisters would see "the divine within nature" and embrace an "emerging new cosmology" that would feed their souls, said Brink. For these sisters, the "Jesus narrative is not the only or the most important narrative. ... Jesus is not the only son of God."

A year later, the Congregation for the Doctrine of the Faith opened its investigation of the LCWR.

The Brink address, noted the resulting doctrinal assessment, "is a challenge not only to core Catholic beliefs; such a rejection of faith is also a serious source of scandal and is incompatible with religious life. ... Some might see in Sr. Brink's analysis a phenomenological snapshot of religious life today. But pastors of the Church should also see in it a cry for help."

Terry Mattingly is the director of the Washington Journalism Center at the Council for Christian Colleges and Universities and leads the GetReligion.org project to study religion and the news.