The Vatican recently finished an exhaustive, three-year inquest, the kind it reserves for its gravest problems. The subject: “American apostolic women religious,” commonly known as nuns.

Almost 400 religious institutions throughout the U.S. were studied as part of this “apostolic visitation,” and a final, confidential report on the nuns’ activities was submitted to the Vatican in December.

Why investigate nuns? Because, Vatican officials said, they were concerned for the sisters’ welfare. But as a former nun -- I left the convent in 1997 after 20 years as a sister in New York, Rome, Washington and Winnipeg, Canada -- I know what the church leaders won’t publicly admit: American nuns frighten them.

I should qualify that remark: Not all U.S. nuns scare the Vatican. The Catholic hierarchy dotes on those who wear long habits with hanging rosaries, unquestioningly obedient nuns who staff Catholic institutions for less than it costs to employ laypeople. But these conservative sisters, who are represented by the Council of Major Superiors of Women Religious, make up less than a tenth of the approximately 50,000 nuns in the U.S. The majority align themselves with the more liberal Leadership Conference of Women Religious.

Second Vatican Council

In 1965, when the Second Vatican Council issued a decree calling all nuns to renewal, most American sisters embarked on a demanding, often painful process of discernment and revitalization. They tried on normal clothes, branched into new ministries and abandoned traditions that kept members childishly dependent on superiors.

Some sisters felt that renewal went too far; others thought it didn’t go far enough. The number of American nuns has shrunk by almost 75 percent since 1965. But those who remain have learned to listen to their consciences, make decisions collectively and, more audaciously, speak their minds -- even if it means opposing the Vatican.

To Rome, these liberal nuns are voices of dangerous dissent: Cardinal Franc Rode, who initiated the new investigation of American sisters, stated on Vatican radio two years ago that U.S. nuns display a suspect “secular mentality” and “feminist spirit.”

In 1976, at age 19, I joined Mother Teresa’s Missionaries of Charity, a traditional community of nuns. Liberal American sisters in polyester didn’t appeal to me; Mother Teresa’s mission to the poorest did. I didn’t realize the community would observe every Vatican decree as though it came directly from God.

I was told that the highest use of my intellect was its unquestioning surrender in obedience; my superiors would always tell me what God asked of me. Eventually, I came to see that the Missionaries of Charity’s anti-intellectualism and rigid separation from the world stunted our work and each sister’s development. Modern nuns’ encouragement of individuals’ gifts and responsibilities no longer seemed like egocentric selfishness -- it seemed like oxygen.

Sometimes I think that if I had joined one of those modern communities, I might still be a nun.

Liberal American sisters are courageous women. Sister Jeannine Gramick, co-founder of New Ways Ministry, continues to advocate for gay rights despite official church efforts to silence her. In 1979, Sister Theresa Kane, then president of the Leadership Conference of Women Religious, greeted Pope John Paul II with a call for dialogue about women’s roles in the church, including priestly ordination, despite the pontiff’s insistence that the issue was closed.

Tragic Choice

In November 2009, the ethics committee at a Catholic hospital in Phoenix on which Sister Margaret McBride served was faced with the tragic choice of aborting an 11-week-old fetus or allowing both mother and unborn child to die. For agreeing with the committee’s decision to terminate the pregnancy to save the mother, McBride was swiftly declared excommunicated. (Two years later, she was reinstated to the church.)

Surveys show that on homosexuality, women’s ordination and the McBride decision, the average U.S. Catholic agrees more with American nuns than with the Vatican.

Sisters speak with a moral authority that the Vatican, tarnished especially by its betrayal of the victims of clerical sexual abuse, can no longer credibly claim.

What the Vatican can claim is power. This month, Father Federico Lombardi confirmed that church leaders have received the report on U.S. nuns but have yet to determine how they will respond. They may choose to do nothing, issue a simple exhortation or --- as more typically happens in response to an apostolic visitation --- deliver punitive prescriptions.

The Vatican retains the power to suppress any group of sisters -- or their activities. One critical issue is property. In the past, the church has sold real estate to pay settlements to the victims of abusive priests. American sisters own the convents, colleges and hospitals that they have built. But if the Vatican were to suppress a community, and no longer list it “in good standing,” it could seize that community’s property and put it under diocesan control. Some groups of sisters are quietly exploring legal options to gain more independence from the Vatican.

American nuns don’t want to fight the official church, but neither are they likely to sacrifice the integrity of their consciences for the sake of peace. Nuns across the country, liberal and conservative alike, tell me the Vatican’s investigation has strengthened them. As each group was asked to account for itself during interviews with the church hierarchy, the sisters’ convictions deepened.

“We know who we are, and we’re going to stand together in our truth, no matter what the Vatican or anyone else says,” the president of a large Midwestern community told me. The investigation also fostered communication across conservative and liberal divisions, softening former antagonisms.

American sisters aren’t a problem for the Catholic Church; they’re an asset. They’re demonstrating new ways to be communities of conscience in the world. With this report, the men of the Vatican can continue to use their power to intimidate anyone who appears threatening, or they can embrace the spirit of dialogue, respect and courage shown by American nuns. I’d love to be pleasantly surprised.

(Mary Johnson, a former sister with the Missionaries of Charity, is the author of “An Unquenchable Thirst: Following Mother Teresa in Search of Love, Service and an Authentic Life.” The opinions expressed are her own.)

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To contact the writer of this article: Mary Johnson at mary.johnson.bv@gmail.com

To contact the editor responsible for this article: Katherine Brown at kbrown114@bloomberg.net