The following is a script from "American Nuns" which aired on March 17, 2013, and was rebroadcast on July 28, 2013. Bob Simon is the correspondent. Andrew Metz and Tanya Simon, producers.
When Pope Francis became the leader of the Catholic Church earlier this year, people around the world asked: what happens now? Can he restore confidence to a Church struggling amid scandal to keep its flock?
To understand just how troubled the Church he inherited is, look no further than the power struggle going on between the Vatican and some of its most popular disciples: American nuns.
The Vatican launched what some Catholics call a "new inquisition" when it accused the official group that represents most nuns in the United States of undermining the Church.
As we first reported in March, the crackdown on the Leadership Conference of Women Religious sparked outrage -- creating yet another rift between those who want the Church to reform, and those who do not.
The new pope of the Roman Catholic Church took his name from Francis of Assisi, the humble saint who inspired orders of priests and nuns devoted to the poor.
And when he stood on that balcony in Rome, few could have been watching him more carefully than the nuns there in St. Peter's Square and in the United States.
In his native Argentina, he showed compassion to the people but also urged Catholic sisters there to promote conservative social values -- very much like what the Vatican has been doing in the United States. That's drawn a lot of attention to sisters like Pat Farrell, who leads the group that represents 80 percent of American nuns.
Bob Simon: You became a nun, I would imagine, for a life of prayer and contemplation and good works.
Pat Farrell: That's correct.
Bob Simon: And all of a sudden you've become a rock star.
Pat Farrell: It's very strange, it's a very strange position to be in.
Bob Simon: Are you enjoying it?
Pat Farrell: No, I'm not someone who prefers to be in the limelight, truthfully.
She was thrust into the limelight last year when the Vatican accused her group of insubordination. After a 3-year investigation, it rebuked the sisters for undermining the Church by publicly disagreeing with the bishops.
[Pat Farrell: We weren't looking for this controversy.]
...And by not vigorously promoting the Church's positions on issues like same-sex marriage and male-only priesthood.
Bob Simon: When you heard that phrase, undermine the Church, were you surprised?
Pat Farrell: Absolutely because the experience we have of ourselves is of trying our best to stand in the middle of very complex situations and issues and to respond in a way that offers hope to people.
Sister Pat spent two decades in El Salvador, ministering to victims of the war -- working in the shadows like sisters everywhere, caring for the sick, as we saw in this inner city clinic, counseling women struggling with addiction and teaching generations of needy children in schools like the Sisters Academy in Baltimore.
But the Vatican says good works aren't the issue -- it's annual meetings like these that the group holds for its members where sisters have given speeches promoting what the Vatican calls "radical feminist themes" that are quote, "incompatible with the Catholic faith."
[Elizabeth Johnson: The Church itself continues to live by patriarchal values that by any objective measure relegate women to second-class status.]