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REPORTER: And I'll tell you this. We've got sunshine and some gorgeous days in the middle of the week here. Wednesday, mid-70s. Upper 70s on Thursday. Upper 70s on Friday. Highs around 80 on Saturday. Lots of sunshine. As of now, No mention of rain in the forecast until Sunday when we have a slight chance of showers and thunderstorms. Things may actually dry out. 62 now.

STEVEN JOHN: The product of more than a year's worth of reporting on the Archdiocese of Saint Paul and Minneapolis. This story has never been told before. Hundreds of hours of interviews and thousands of documents make clear that church leaders knew they had abusers in the priesthood, and they did everything in their power to keep the situation quiet. Meanwhile, they reassured the faithful and the media that clergy sexual abuse was a thing of the past.

SPEAKER 1: He should have said to me, your children could be in danger. OK, father. OK.

JENNIFER HASELBERGER: I was also just concerned that these people were in ministry. And that people were at risk.

SPEAKER 2: Today, we decided it is imperative for us to reopen the investigation.

SPEAKER 3: The St. Paul Police Department is seeking victims of sexual abuse perpetrated by members of the Catholic Church.

SPEAKER 4: When I arrived here seven years ago, one of the first things I was told is that this whole question of clerical sexual abuse had been taken care of.

SPEAKER 5: They were responsible to be the shepherds. They're the ones who were supposed to have stopped it. They had all the information, and they chose not to stop it.

STEVEN JOHN: In this special report, "Betrayed by Silence," we'll take you inside the cover-up led by three archbishops, to see how and why the church protected priests who sexually abused children. Madeleine Baran reports.

PRIEST: Hail Mary, full of grace, the Lord is with Thee.

MADELEINE BARAN: The Cathedral of Saint Paul dominates the city's skyline. The archbishop who built the seat of power a century ago is remembered in the street that leads to the State Capitol below, John Ireland Boulevard. There are still more Catholics in Minnesota than any other religion. But the majesty of the cathedral and the faith of parishioners were rocked by a whistleblower in 2013. 39-year-old Jennifer Haselberger grew up going to mass at Saint Casimir's parish on St. Paul's east side, praying for the archbishop.

JENNIFER HASELBERGER: Like many Catholics, when we're at mass, my mind still defaults towards the part in the eucharistic prayer where we pray for our bishop. I still hear the priest of my childhood saying, John R. Roach, our bishop.

MADELEINE BARAN: Haselberger would learn that the men of the church she'd prayed for had exposed children to abusers, then used the money and the power of the church to keep things quiet. Although she was a devout Catholic, Haselberger was something of an outsider in the chancery, the first canon lawyer who wasn't a nun or a priest.

For five years, she served as Archbishop John Nienstedt's top advisor on church law. She handled the church's most secret documents and stumbled across troubling information about sexual abuse by priests. She alerted church leaders that children were in danger. Church leaders dismissed her warnings. In April of 2013, Haselberger resigned. But she felt burdened by what she knew. In July, she called MPR News.

JENNIFER HASELBERGER: I absolutely believe that we have priests in our parishes currently who have either committed acts of sexual abuse against a minor or who we have more than adequate reason to believe are capable of doing so.

MADELEINE BARAN: Haselberger's revelations stunned parishioners. No one at such a high level in any diocese in the Catholic Church in the United States had ever come forward to expose the cover-up. She revealed a carefully guarded web of secrets and a culture bred to protect the church at any cost. To some, it was an old story.

Sexual abuse in the Catholic Church has been in the news for decades. But what Haselberger revealed was that what most people think about the scandal is wrong, especially in the Twin Cities. Church leaders here had claimed to be national leaders on the issue and avoided scrutiny by assuring parishioners and reporters the problems lay elsewhere.

One by one, MPR News stories exposed what the archdiocese had tried to keep secret for decades. The fallout was immediate. The vicar general resigned within days. Police opened criminal investigations. Catholics held protests. And Nienstedt canceled his public appearances. Nienstedt and former Archbishop Harry Flynn declined to be interviewed. In mid-November, Nienstedt recorded a statement announcing he would bring in an outside firm to review clergy files.

JOHN NIENSTEDT: We also want to assure the public that in all cases under my leadership, we have complied with mandated reporting requirements to law enforcement. Serious mistakes have been made in the archdiocese's handling of abuse cases.

MADELEINE BARAN: It was something victims have heard before.

CHERYL HERRITY: Mistakes have been made. Mistakes? I mean, I just wanted to scream it. Unbelievable! They are unable to tell the truth. Call it what it is, sexual crimes against little children.

MADELEINE BARAN: Cheryl Herrity's son, Brian, was one of the first local victims to come forward to police more than 30 years ago, back when it was unthinkable that a priest would rape a child. Cheryl and her husband, Jeff, shake their heads as yet another bishop pledges that protecting children is his number one priority. They think the problems uncovered by Haselberger can be traced to an arrogance that stretches back decades.

Their son, Brian, was abused by Father Gilbert Gustafson in the late '70s and early '80s when the family attended St. Mary of the Lake church in White Bear Lake. Brian told police the priest forced him to perform oral sex. One time, it even happened on the family's porch while his mother watched TV inside. As an adult, Brian struggled with memories of the abuse and lost himself in drugs and risky sex. At age 28, he made a cassette recording in his bedroom.

BRIAN HERRITY: Hi, my name is Brian Herrity. And the reason why I'm making this tape is because I've-- I know I'm dying of AIDS. And I feel a little awkward doing this, but I hope that in the future, whoever happens to come across this tape and maybe if God puts this tape in your life for a reason, that it would have some impact on somebody else's life.

MADELEINE BARAN: Brian talked about the abuse.

BRIAN HERRITY: And at 14 years old, I well, seen a lot of life. I've been sexually abused by a Catholic priest for five years, 4 and 1/2 years. Tore up in court systems. Left even feeling lonelier than I started.

MADELEINE BARAN: Brian Herrity died of AIDS a short while later from a sexual contact as an adult. His father, Jeff, says the abuse destroyed his son.

JEFF HERRITY: I watched my son, who was a loving little boy, who used to get on my lap and watch football and giggle and just very innocent go from that to something I couldn't even explain. And he died of AIDS. They murdered my child.

MADELEINE BARAN: The Herritys told the archdiocese about the abuse in 1982. And Archbishop John Roach sent Gustafson away for treatment. In the '80s, the church was used to handling problems internally to keep things quiet. Church leaders hired therapists who told them what they wanted to hear, that priests could be rehabilitated.

But bishops had known since the '60s that treatment failed. When priests came back, they would often abuse more kids. Police wouldn't learn about Gustafson's abuse until Brian's therapist reported it. Tom Foley was the Ramsey County attorney at the time and a Catholic himself. He remembers facing resistance from church leaders who did not want criminal charges brought against one of their own.

TOM FOLEY: Several priests or monsignors met with me and were trying to persuade me that treatment would be a better option and that Father Gustafson should not be prosecuted as a criminal. I disagreed. I thought these were outrageous activities, and that he should be prosecuted.

MADELEINE BARAN: Gustafson's attorney told police the priest probably had sexual contact with fewer than 10 kids. Gustafson was only charged with abusing Brian. He pleaded guilty and was sentenced to six months in jail. Jeff Herrity remembers the show of support Father Gustafson got in court.

JEFF HERRITY: They had all these clergy in the back without their vestments on, hugging and kissing Gustafson, feeling bad for him.

MADELEINE BARAN: Herrity saw another priest from their parish sitting over on Gustafson's side.

JEFF HERRITY: And after it was all over, I went over to him. And I said, why aren't you with us? What are you doing with them? No answer.

MADELEINE BARAN: So there are no priests with you?

JEFF HERRITY: No, no, no. No one. I didn't get no hugs. But I wouldn't want a hug from them anyhow. But, I mean, they're over there hugging and crying. And what's that all about?

CHERYL HERRITY: Yeah. Here we are sitting there, the three of us alone. That was one of the most painful scenes that I've been a part of.

MADELEINE BARAN: The Herritys believed they were alone, that the abuse was an isolated incident. But the church knew it wasn't. In the 1950s, a cleric who treated pedophile priests realized he couldn't cure them. He proposed an unusual solution. The Catholic Church should buy a deserted island in the Caribbean and warehouse pedophile priests far away from children.

Church officials said no. The Gustafson case in Minnesota in 1983 did not attract much attention. That same year, a much bigger scandal was brewing in Southern Louisiana. The man sent in to control the scandal would later emerge as a key figure in the Twin Cities and on the national stage-- Bishop Harry Flynn.

HARRY LYNN: The events in Lafayette inspired the first discussion among the bishops of this problem on the national level.

MADELEINE BARAN: Flynn would use his claims that he'd healed the Diocese of Lafayette to advance his career. His friends would talk about how he'd trekked across bayous and dirt roads to reach out to victims. The Catholic hierarchy would later use Flynn to save it from an even worse scandal years later. There was just one problem, Flynn's story wasn't true.

[CHURCH BELL RINGS]

The Louisiana case was a disaster. Deep in Cajun Country, a young priest named Gilbert Gauthe had been caught abusing hundreds of boys in rural churches along the bayous and sugarcane fields. Gauthe had won the trust of parents by taking their sons on camping trips. He held altar boy practices at six in the morning as an excuse for boys to sleep over.

At night, in the rectory, Gauthe raped the boys, forced them to perform sex acts on each other, and took pictures on his Polaroid camera. Parishioners soon learned the bishop knew of complaints about Gauthe for years and had moved him from parish to parish.

RAY MOUTON: The pressure was coming all the way from the Vatican. Get this over with. We don't want a trial. We don't want the publicity.

MADELEINE BARAN: Ray Mouton was the attorney hired to defend Gauthe. He now lives in France. Mouton was so appalled by his client's actions that he made an unusual request.

RAY MOUTON: I asked the diocese to let us identify every victim we could. There were so many. He testified under oath in a deposition that there were probably more than 200. But to identify every possible victim by using school yearbooks, old altar boy rosters, and to reach out to those victims.

MADELEINE BARAN: The diocese refused.

RAY MOUTON: And from that point on, I was pretty much persona non grata.

MADELEINE BARAN: Gauthe was sentenced to 20 years in prison. The diocese offered more than $1 million to none families to settle their cases quietly. But victims kept coming forward, not just about Gauthe but other priests as well. The elderly bishop who'd covered up the abuse fumbled in his response. He froze talking to victims. He gave a disastrous interview. And the local paper called for him to resign.

The Vatican Embassy watched with growing concern as it became clear the bishop was in over his head. He needed to be replaced. The Vatican turned to a parish priest in Upstate New York named Harry Flynn. Embassy official Thomas Doyle led the search.

THOMAS DOYLE: Flynn's name came on the radar fairly quickly because we did know who he was. We knew of him. And he did have this reputation. I believe he had given priests retreats and conferences, that kind of thing. And he had a reputation of being a really good guy, very pastoral, very compassionate. And that's why we focused on him rather than a company man who would be purely administrative.

MADELEINE BARAN: Flynn arrived in Lafayette in 1986. Doyle urged him to meet with Ray Mouton, the priest's attorney.

THOMAS DOYLE: Because I said Ray knows the situation better than anyone else. He knows the ins and the outs. He knows the deep layers. And he can help you more than anyone else.

RAY MOUTON: Flynn arrived in Lafayette. I saw the media. And I heard his statements. And my phone didn't ring. My office was four blocks from his office. So I wrote him a letter, very nice letter. I welcomed him to Lafayette and stressed that it was urgent that I meet with him.

And he ignored the letter. He did not want to meet with the person that the canon lawyer in the Vatican Embassy directed him to. He met with the diocesan lawyers and took their tact.

THOMAS DOYLE: I mean, the clerical arrogance came out immediately.

MADELEINE BARAN: Doyle was disappointed. His handpicked bishop was a company man after all. Doyle was soon forced out of his job for demanding the church protect children. Once Flynn arrived, he directed attention away from the scandal. Clergy abuse faded from the headlines. Flynn welcomed Mother Teresa for a packed event at the Cajundome. He said a special mass for lawyers. The new yorker even found time to travel to the tiny town of Delcambre to bless the shrimp fleet.

HARRY FLYNN: Hey, how y'all doing?

MADELEINE BARAN: Mike LeBlanc runs a gas station where the shrimp boats fuel up. He says it was the first time that a bishop had delivered the blessing instead of the local priest.

MIKE LEBLANC: I don't know why he came that year, but it was something nice, real nice.

MADELEINE BARAN: A 15-minute drive from Delcambre through the bayous and sugarcane fields is a church where Father Gauthe terrorized so many children. Wayne and Rose Sagrera run an alligator farm here. Three of their sons were abused by Gauthe. Rose Sagrera says some of the families formed a prayer group.

ROSE SAGRERA: We would pray and try to get some healing. And so when Bishop Flynn came to this area, well, he also started coming to this meeting. And that's fine. It would broke up the meeting. We stopped having the prayer meeting when it just wasn't going anywhere. And it was causing more pain than healing.

MADELEINE BARAN: The Sagreras wanted Flynn to reach out to parents who were in denial that their children were abused and try to get them help. Wayne Sagrera says Flynn made it clear he was there to protect the church.

WAYNE SAGRERA: In private, he said that they were wrong. But he would not publicly get out and say it because of the vows he'd taken and that the church must come first.

MADELEINE BARAN: In Bishop Harry Flynn's account of his years in Lafayette, he often depicted himself as a healer who subjected himself to the humiliation of apologizing for the sins of priests. Years later, at a. conference in New York, Flynn said he learned an important lesson in Louisiana.

HARRY FLYNN: The bishop cannot look at this situation only with the eyes of the priest. With psychological and spiritual empathy, he must look at the pain confronting him as much as he possibly can with the eyes of the victim and the eyes of the parent whose child has been molested.

MADELEINE BARAN: But in Louisiana, the Sagreras say the Flynn they met was cold and emotionless and couldn't seem to grasp the suffering of victims and their families. And yet, Flynn was popular among parishioners elsewhere in the diocese.

ROSE SAGRERA: People who weren't involved were very taken by him, and that was the greater majority. And so he did that kind of healing.

WAYNE SAGRERA: It's hard for someone who was not directly involved to realize the hurt, the pain. So, yeah, I'm sure some of those people, yeah, well, it's taken care of now. The bishop came and everything's good. But I don't see how healing can be done if you don't deal with the people who are involved.

MADELEINE BARAN: The Lafayette diocese paid out more than $4 million in settlements to the Sagreras and other families. But Flynn's diocese later sued its insurers and got most of its money back. The insurance agency fought back and obtained thousands of internal church documents that showed a massive cover-up that went far beyond the actions of one priest.

In the files were the names of dozens of priests accused of sexual misconduct. No records exist of any reports to police under Flynn. Those revelations would likely have ruined Flynn's career, but no one ever found out because the lawyers had the entire case sealed.

Instead, Flynn created a myth about how he healed the Diocese of Lafayette. Thomas Doyle says the Vatican hierarchy admired Flynn's work. In 1994, They sent Flynn to Minnesota to serve as the new archbishop of Saint Paul and Minneapolis.

THOMAS DOYLE: They wanted him to go there as a promotion. Because keep in mind, by that time, the whole Tom Adamson thing was known in Minneapolis, St. Paul. And that was a huge mess as well.

MADELEINE BARAN: Tom Adamson was a priest from the Winona Diocese who'd sexually abused boys throughout Southern Minnesota. The Adamson case was the second national abuse scandal to hit the Catholic Church. It drew the battle lines in the Twin Cities for the next 30 years.

It began in 1984 when a young attorney named Jeff Anderson got an odd phone call. A Catholic couple told him their son had been abused by a priest. They showed him a check for about $1,500 that they'd received after confronting the archdiocese. They wanted to know if they should cash it.

JEFF ANDERSON: And it wasn't making sense to me at all that they send the money unsolicited. I just knew the whole thing stunk.

MADELEINE BARAN: Anderson did not know much about the Catholic Church, and a search of court records for lawsuits came up empty. But Anderson did know something about taking on powerful institutions. He'd represented gay men beat up by police at bathhouses and an African-American man who was charged with trespassing for using a bathroom at a wealthy, all white church. Anderson walked up to the chancery with his lawsuit.

JEFF ANDERSON: The next day, the lawyers called me and said, What do you want? I said, well, I want the priest out now. And they said, OK, we're removing him today. I said, good. And they said, what else do you want, meaning money? And I said, I want answers. I want to know who's in charge. I want to know why whomever is in charge here allowed this priest to continue.

And they said, well, the Archbishop John Roach is the one that's in charge. And he makes all the decisions. And I said, well, then I need to ask him questions under oath and take his deposition. And they said, that's impossible. That would never be done. That has never been done. That's not going to happen.

MADELEINE BARAN: Anderson threatened to file the lawsuit in court if Roach refused to talk. The threat worked. The church agreed to answer Anderson's questions Under oath in 1986, Roach and Winona Bishop Loras Watters denied knowing about Adamson's sexual interest in children.

But Anderson had done his homework. He tracked down a father who said he told Watters a decade earlier that Adamson had abused his son. Roach had dismissed another father's complaint about Adamson a few years later. Anderson had caught two of the most prominent men in Minnesota in a cover-up. Roach's men called Anderson to settle.

JEFF ANDERSON: They said, we want to offer $1 million with the usual confidentiality agreement. And I said, did you say usual? They said, yes, usual is what we do. And I said, you mean, you've done this before? They said, well, yes, this is how we-- this is how we handle settlements like this.

MADELEINE BARAN: Anderson suspected that Adamson had abused dozens of kids and that he wasn't the only priest Roach was protecting. But with a secret settlement, no one would know. That night, Anderson couldn't sleep. In the morning, he went to see his client, Greg Riedle, and asked him to do something he knew sounded crazy. Turn down the million dollar settlement and expose the cover-up in a public lawsuit.

JEFF ANDERSON: He said, that's a ton of money. I said, I know. It's huge. But it's wrong. And what they've done is wrong. And there's other kids, Greg. And he said, oh Jeff, I know. He said, OK, I trust you. I trust you. Turn it down, but turn it down quick before I change my mind.

MADELEINE BARAN: Anderson rushed over to the courthouse to file the lawsuit. Then he called every reporter he knew. On a February morning in 1987, Minnesotans awoke to front page headlines revealing Catholic leaders had protected a predator. After the secrets were out, Riedle reached a $1.1 million settlement with the church. Anderson took another Adamson victims case to trial two years later.

REPORTER 2: Jurors have been listening to closing arguments in the case of a man who is suing the Catholic Church because he was sexually abused by a priest.

MADELEINE BARAN: The jury awarded Anderson's client $3.5 million, most of it in punitive damages that insurance would not cover. The press mobbed Anderson outside the Anoka County Courthouse.

JEFF ANDERSON: In their verdict, they have sent a message to the defendant, Diocese of Winona and the archdiocese and perhaps every diocese in this country. And to my knowledge, there is no diocese in this country in the church that has ever been held to account in punitive damages for wrongful conduct of this kind. And so in that sense, it's a real significant message.

MADELEINE BARAN: A judge later reduced the amount. But Anderson has been battling the church ever since. Roach was stunned by the verdict as reported by MPR News.

REPORTER 3: Archbishop John Roach of the Twin Cities held a news conference after the verdict was announced. He said the entire society was ignorant about child sex abuse 10 years ago and so were church leaders. Roach gave his assurances that the church has instituted new policies in the past few years. And he says it's highly unlikely this kind of long standing sex abuse could happen again.

JOHN ROACH: We follow the best advice that we had available to us at that time. And we followed the best knowledge that we had of the nature of pedophilia. Our decisions certainly did not represent either willful indifference or reckless employment.

MADELEINE BARAN: But it was willful. Roach was a powerful figure in St. Paul. Decisive, confident, and beloved by parishioners. Roach was also fiercely loyal to his priests. Rather than report allegations to police, he transferred abusers from one parish to the next and quietly sent some of them to treatment. To victims, he offered regret and talked about the importance of healing and moving on. Victims, for the most part, stayed quiet. The scandal was contained, but not for long.

[MUSIC PLAYING]

STEVEN JOHN: This is MPR News Presents with a special report, "Betrayed by Silence-- How three archbishops hid the truth."

REPORTER 4: James Porter of Oakdale, Minnesota, has pleaded guilty to molesting 28 children in the state of Massachusetts. Porter entered the plea today.

MADELEINE BARAN: Former priest James Porter was arrested at his home in Oakdale in 1992 and extradited to Massachusetts.

COURT CLERK: James Porter on a diamond 31285 charged with indecent assault and battery on a child under the age of 14. How do you now plead? Guilty or not guilty?

JAMES PORTER: Guilty.

MADELEINE BARAN: Bishops responded to the Porter scandal by creating a National Committee to review the church's response to clergy sexual abuse. They appointed Archbishop Roach and the bishop from Lafayette, Harry Flynn.

Victims were beginning to get organized too. They were meeting across the country as part of a group called the Survivors Network of those Abused by Priests. David Clohessy of St. Louis was the group's national director. In 1993, he picketed with other victims outside of a bishops meeting until they were invited inside to meet with Flynn and two other bishops.

DAVID CLOHESSY: And it was very emotional. People were really pouring out their hearts and souls because clearly, people were-- all of us were in pain. And all of us saw this as a pretty rare opportunity. And all of us believed in our hearts and souls that these were the men who could make a real difference. These were the guys who really could get our predators out of ministry, who could tell the truth, who could warn the public, who could call the police, who could do real outreach.

MADELEINE BARAN: Clohessy says Flynn's body language made him think he was deeply moved by what he was hearing.

DAVID CLOHESSY: I remember his brow being furrowed, and he made great eye contact. And he kept his hand off and on his chin and would say hmm, oh, and shake his head back and forth. And he really did look to be the most sympathetic of the three.

MADELEINE BARAN: Flynn's meeting with victims impressed his fellow bishops. And when Twin Cities Archbishop John Roach decided to retire, he recommended Flynn replace him.

[CHOIR SINGING]

REPORTER 6: There was great pomp and circumstance at the St. Paul Cathedral as Bishop Harry Flynn was welcomed as coadjutor of the Saint Paul Minneapolis Archdiocese.

MADELEINE BARAN: In 1994, Flynn brought what he learned in Louisiana to Minnesota. He'd created a playbook for how to handle the abuse scandal, expressed concern for victims, hire aggressive attorneys, and disclose nothing. And like Roach before him, stay loyal to priests and put the church's reputation above all else.

Flynn immediately pushed back against victims attorney, Jeff Anderson. Anderson had sued the archdiocese on behalf of a man who said he was sexually abused as a child by Father Robert Kapoun. Dale Scheffler said Kapoun had taken him to his cabin when he was 13 and sexually assaulted him in a lake and while he was sleeping. Outside a Hennepin County courtroom, Scheffler begged Flynn to remove Kapoun as pastor.

DALE SCHEFFLER: Archbishop, I come here today to ask you to please remove him. How can you go on living and knowing that they're doing this. Please, I'm asking you to remove these people, to remove all these priests that are doing these to these kids that are getting hurt.

MADELEINE BARAN: Later that day, Flynn removed Kapoun but stood by the priest's claim of innocence. The jury awarded Scheffler $1.2 million. But the case was overturned on appeal because the statute of limitations had run out. What Flynn did next signaled he was willing to play hardball with victims.

The archdiocese billed Scheffler for its legal costs, though it never collected. Flynn's attorneys wanted to put a stop to Anderson's lawsuits. In 1996, they convinced the Minnesota Supreme Court to drastically limit the window for victims to sue.

Victims now needed to file before they turn 24. Since most victims don't come forward for decades, the ruling slammed the courthouse doors shut. Anderson had to watch from the sidelines as Flynn promised to kick out offenders and protect children. He suspected Flynn was lying, but he couldn't prove it without the ability to sue.

JEFF ANDERSON: People didn't have any way of knowing what we knew and believed. And I had no way of showing them or proving to them in the courts or through the media that they weren't any better, they weren't any cleaner, that they were doing the same things now that they had done in the past. They're just doing them a little differently. And their PR machines were effectively convincing people that the problem was in the past when it was very much in the present.

MADELEINE BARAN: With Anderson out of the way and reporters convinced the story was over, Flynn was free to handle abusive priests however he wanted. He kept all of them in the priesthood and never called police. The cover-up continued. So why would the church protect priests who've raped children? The answer lies within the culture of the organization itself.

Like the military or police, the priesthood is a closed group that protects its own. It's a brotherhood that defends the institution above all else. But what makes the priesthood more secretive than other groups is the requirement of celibacy.

RICHARD SIPE: Celibacy is a sham.

MADELEINE BARAN: Richard Sipe is a therapist and former Benedictine monk. He's an international expert on sexuality in the priesthood. Sipe says celibacy doesn't cause pedophilia, but the priesthood can be a refuge for predators. Sipe says total celibacy-- no sex, no masturbation, no sexual thoughts-- is nearly impossible for most priests. And those sexual sins drive the cover-up.

RICHARD SIPE: It's a secret society. And this is a dimension of the secret society. I know this about you. You try and do this to me, I will reveal this about you. So let's just live in peace and keep our secrets and go on.

MADELEINE BARAN: Documents show that for some priests in the Twin Cities, those secrets involve sex with prostitutes, married parishioners, or even other priests. For others, they involve crimes against children. Most of the time, those children are boys. A study funded by the Catholic Church in 2002 found about 80% of the time the victim was male, most of them pre-teens or teenagers. Sipe says Catholic parishioners expect some secrecy because it serves a purpose in the church.

RICHARD SIPE: You go into a confessional to a priest and you expect him to keep your name and identity and your faults secret. It's a great service to humanity in terms of being able to trust at least someone else with the deepest truth of yourself.

But what happens is that the church spreads that. It's called a creeping infallibility and a creeping secrecy so that everything that would cause scandal is now kept secret and supposed to be kept secret. And by the way, if you don't keep those secrets, father is abusing these boys, you're ostracized.

MADELEINE BARAN: There are also more practical concerns for bishops to consider. They want to protect the financial assets of the church from lawsuits. So in this closed society filled with sexual secrets, victims who speak out are treated as threats. Archbishop Flynn's right hand man in managing victims and abusers was an ambitious priest named Kevin McDonough.

McDonough had served as vicar general under Roach and continued in that role under Flynn. Nobody knew more about the clergy sex abuse scandal and the cover-up than McDonough. The politically savvy priest showed sympathy to victims and claimed to be an expert on abuse in this nationally distributed training video the archdiocese made in 1992.

KEVIN MCDONOUGH: Abuse is an old problem newly understood. The reality is that sexual misconduct has existed for a long time. One of the most positive things is that in the last decade or so, there's been an explosion of understanding in the church and in the general society.

MADELEINE BARAN: McDonough also spoke eloquently in the media about the church's effort to restore trust. Here he is in an MPR News story in 1990.

KEVIN MCDONOUGH: We have to work hard to make ourselves trustworthy again. I happen to think my own prejudices that we're trustworthy. But people have to come to believe that. The only way they're going to believe that is to have some experience with us. That's probably going to take the better part of a decade. I kind of view what we're doing in this period as making up for a lot of bad practice in the past.

MADELEINE BARAN: McDonough's line was always the same. This scandal is behind us. It was his message in the '80s, the '90s, the 2000s, and even last year. McDonough's charm and skill as a strategist would help protect the archdiocese as the worst scandal in the US Catholic Church exploded in Boston in 2002.

REPORTER: This is the 10 o'clock news on Boston's WB 56.

REPORTER: Boston today, a community in shock.

REPORTER: NBC News in depth tonight, crisis in the church, sexual abuse of children by priests.

REPORTER: And yet another apology from Boston's pulpit for failing to protect children from a pedophile priest.

MADELEINE BARAN: The Boston Globe broke the story of how powerful men had protected a serial predator in one of the wealthiest archdiocese in the country. Bishops panicked as reporters uncovered similar scandals in other dioceses across the country. The faith of the nation's 65 million Catholics and the church's wealth and reputation were on the line. Bishops needed someone with credibility to restore trust.

Harry Flynn was the obvious choice because he hadn't been tarnished by past scandals. His stories about his time in Lafayette had established his reputation as the healer bishop. He'd managed to silence the scandal without being accused of a cover-up. He'd also protected the church in St. Paul. Bishops appointed Flynn to lead the National Response at a conference in Dallas.

HARRY FLYNN: This is a defining moment for us this morning as bishops, a moment for us to declare our resolve once and for all to put a plan in place and to commit ourselves to that plan so as to root out a cancer in our church.

MADELEINE BARAN: Flynn even tried to turn the scandal into a positive for the church.

HARRY FLYNN: There is no institution, no institution that has looked at this phenomenon in such a comprehensive manner. So in order to come up with some good results, protection for the future, and also for us to be some kind of a witness to the rest of our society, we must do this right. And it's going to take time.

MADELEINE BARAN: Flynn headed a committee that drafted a national policy on clergy sexual abuse called the Charter for the Protection of Children and Young People. The media hailed it as a historic document.

REPORTER: After much forceful debate, a new plan to rid the church of abusers. The bottom line, for even a single act of sexual abuse of a minor past, present, or future, the offending priest or deacon will not remain in ministry.

MADELEINE BARAN: But the Charter was not a watershed document. Bishops always had ways to remove abusers from ministry. Just one year earlier, Pope John Paul II had ordered bishops to send all abuse cases to the Vatican for possible dismissal. It was a chance for bishops to clean house.

The Charter was more of a public promise than anything else, a promise made by the same bishops who had just been caught covering up abuse. There was no accountability for bishops. They opted not to punish themselves if they failed to follow it. Throughout the Dallas conference, bishops expressed regret that children had been abused. They invited David Clohessy, the victim who had met with Flynn nearly a decade earlier, on stage to speak. Clohessy described the sexual abuse crisis as an infection within the church.

DAVID CLOHESSY: Don't settle for cheap talk, for grave expressions of concern. Don't settle for eloquent apologies. And don't settle for pledges to do better in the future. Let's not replace a dirty bandage over an infection with a bright new, clean, bigger and broader bandage.

MADELEINE BARAN: Back in St. Paul, Flynn kept the infection covered up. He didn't ask the Pope to defrock a single abusive priest. No one called police. And prosecutors didn't ask any questions. If Flynn had come clean, parishioners would have realized that the archdiocese that claimed to be a national leader had covered up abuse for decades, and Flynn's reputation would have been ruined.

While Flynn traveled the country praising the Charter, back home, Vicar General Kevin McDonough was busy managing the cover-up. McDonough negotiated with some abusers to take early retirement. Flynn could have forced the priest to retire, but he thought a voluntary approach would be more discreet.

From 2002 to 2011, secret deals and other payments for clergy misconduct would cost the archdiocese nearly $11 million. Flynn's demand for secrecy gave abusers tremendous leverage. Many demanded money in exchange for so-called voluntary retirement. One priest got a $20,000 check for his mortgage. Others got special housing allowances and extra monthly checks.

One of the best deals went to the Reverend Gil Gustafson, who had pleaded guilty in the '80s to sexually assaulting Brian Herrity, the boy who later died of AIDS. Flynn said Gustafson's sexual abuse of a child rendered him medically disabled and he should receive extra money.

In a secret deal, Gustafson agreed to make certain that no one would find out he was still a priest. And the church and Gustafson agreed not to defame each other. In sworn testimony in May of 2014, Flynn falsely claimed that Gustafson was no longer a priest and defended the payments.

HARRY FLYNN: He would not be receiving payments for pedophilia. He'd be receiving payments because he victimized and is not able to work at an adequate position any more. That's why he would receive payments.

MADELEINE BARAN: The names of Gustafson and other abusive priests disappeared from public church directories. McDonough wrote a letter to abusers in 2002 read here by an MPR News staffer explaining he made the change so no one would find out the men were still priests.

MPR NEWS STAFF: When the 2003 edition of the Minnesota Catholic directory appears, your name will not be in it. In the highly controversial atmosphere of today, we thought that it was necessary to air on the side of caution. I do not relish the idea of a reporter standing outside your home holding a copy of the directory and claiming that you are being secretly kept in the priesthood in violation of the charter.

MADELEINE BARAN: Meanwhile, McDonough assured the reporter that the church would be more open and accountable from now on.

KEVIN MCDONOUGH: We'd be the world's biggest fools to try to gloss over at this late stage in the discussion. Now, some of us foolish, of course. But I think we've learned a great deal the last couple of years in terms of the need for public transparency and for the pure light of open public discussion.

MADELEINE BARAN: As the cover-up continued, the pace picked up. McDonough handled so many allegations that he admitted that sometimes he lost track. In hundreds of memos from 2002 to 2008, McDonough downplayed sexual behavior by priests. He developed his own language for talking about the cases and appeared to consider himself something of an amateur psychologist.

MPR NEWS STAFF: August 8, 2005, I believe that it is likely that he did kiss them without any conscious sexual intent, at least in part because he was largely unaware of that dimension of life at that time. Nevertheless, both young women later recalled the kisses as confusing and apparently sexual.

August 3, 2006, I do not believe that Father Wehmeyer actually goes to these parks to pick up other men. Rather, he likes to be around the environment where such things are happening, since it gives him some sort of thrill. October 22, 2004, the publicly observed behavior is not, as some at All Saints apparently fear, the tip of some awful psychosexual iceberg, but a previously reinforced pattern that now must be changed.

MADELEINE BARAN: Jennifer Haselberger, who had later come forward as a whistleblower, got her first glimpse of McDonough's handling of the abuse crisis in 2006. Haselberger was working for the Diocese of Crookston at that time, and the bishop asked her to tell a priest that the Pope had kicked him out of the priesthood. A letter from a chancery official said the priest had been accused of sexual contact with women and at least one teenage girl under his pastoral care. Haselberger was surprised to find the priest working in the archdiocese. She called McDonough.

JENNIFER HASELBERGER: The first thing that surprised me is when I got there. And I had the decree of dismissal. And I kind of said, OK, this is what we need to do. He should be given the opportunity to review it. And I kind of said, well, not that I need to tell you this, you've probably been through this before. And he said, actually, can I take a look at this because this is the first time I've seen one.

MADELEINE BARAN: Haselberger was shocked. She assumed the archdiocese would have kicked out many priests. Privately in memos McDonough made, a stunning admission. He never really understood how to follow the Charter. He said he missed the national training because of a snowstorm. In the meeting to dismiss the Crookston priest, Haselberger says McDonough took over.

JENNIFER HASELBERGER: While I was there to communicate the dismissal and the fact that this was a penalty that was being appropriately applied for some egregious offenses against the sacraments, against these individuals, against really the fabric of the church, the message that was actually communicated by Father McDonough to the priest was that while this was an external decision, internally, he would remain a priest forever.

Father McDonough looked at him and put his hand over his heart and said, you're a priest forever in here. And I don't remember any reference to the victims or the people who had been hurt.

MADELEINE BARAN: Next, Haselberger went to tell one of the victims that the Pope had reviewed the case and decided to dismiss her abuser.

JENNIFER HASELBERGER: She asked me, how is he? How did he deal with that? I mean, he made a difference in her entire life, having encountered her as a young girl. The effects of that abuse could be seen throughout the whole trajectory of her life. But yet she still had that level of compassion for him as a person to ask. Again, all of that missing from the other meeting.

MADELEINE BARAN: McDonough also dealt with dozens of victims who came forward after the Boston scandal broke. In person, McDonough was warm and empathetic. He sometimes wept. Privately, however, he funneled his meeting notes to the archdiocese's attorneys to look for details that would help the church if it were sued.

Memos show McDonough played good cop/bad cop with victims. For example, he'd offer a low financial settlement and then claim that the archbishop wanted to be more generous. All the while, memos showed McDonough was orchestrating the entire thing. McDonough was skilled at sizing up victims and the liability they represented.

One man went to McDonough after the Boston scandal about abuse he suffered in 1961 when he was 11 years old. Tom Mahowald served as an altar boy at Guardian Angels Church in Hastings. One morning after mass, Mahowald says Father Patrick Ryan asked him to follow him into the basement to help move some heavy boxes. The priest cornered him.

TOM MAHOWALD: And he whispered in my ear, God wants you to do this for me. And that kind of froze me. And the next thing I knew, my pants were off and he was raping me.

MADELEINE BARAN: As Mahowald struggled to get away, the priest reached down and crushed his testicles. Mahowald said a church board told him at that time his story was unbelievable. He later had three surgeries to try to repair the damage to his testicles. He has been unable to father children.

Mahowald says at first, McDonough treated him well, and the church paid for him to go to a therapist. The archdiocese also paid his insurance premiums and sent him to a 10-day retreat in Kentucky for victims of clergy sexual abuse. But Mahowald was still seeking answers. He interviewed McDonough on video in 2004.

TOM MAHOWALD: We're here at the Archdiocese of Saint Paul and Minneapolis today to talk to Father Kevin McDonough, vicar general.

KEVIN MCDONOUGH: I'm the archbishop's chief of staff.

MADELEINE BARAN: On tape, McDonough described how the church's understanding of sexual abuse had evolved over the decades. He said in the '60s and '70s, the period when Mahowald said he was abused, the church did not recognize the long-term profound damage to child victims. Sexual abuse was viewed as a sin on the part of the priest. When the priest was confronted, he'd cry and promise not to do it again. McDonough says the church started to wake up when it got sued.

KEVIN MCDONOUGH: And frankly, there's nothing that gets one's attention focused as clearly as being sued for mistakes, oversight, negligence, wrongdoing you've committed in the past. The interview ended on a positive note.

TOM MAHOWALD: Well, thank you, Father Kevin. I'd just like to say in closing, I think you treat me very fairly and openly. And I thank you for taking a leadership role in this issue.

KEVIN MCDONOUGH: Tom, I've had a lot of respect for you. And you've never treated me with anything less than human respect and Christian. And so I think that's been a good thing back and forth. I'm grateful for the chance to respond to your questions.

MADELEINE BARAN: Two years later, Mahowald approached the archdiocese for settlement. He wanted to use a mediator who specialized in restorative justice. That's when Mahowald says his relationship with McDonough changed.

The archdiocese hired private investigator, Richard Setter, to look into Mahowald's claims. Setter handled many such cases for the church. He interviewed Mahowald about the abuse. And Mahowald offered medical records dating back to the late 1960s.

He also asked Setter to interview his brother and sister, who knew that he had suddenly quit being an altar boy. Setter did not call them. He determined that the abuse could not be substantiated. Setter said there was not enough evidence to link Mahowald's injury with the abuse because the hospital had destroyed its records from the early '60s.

TOM MAHOWALD: They hired somebody that worked for them to prove me wrong.

MADELEINE BARAN: McDonough wrote a letter to Mahowald telling him the archdiocese would be cutting off its financial support at the end of the month.

MPR NEWS STAFF: I hope this information, painful as it is, may in its own way be helpful to you in your process of self-understanding.

MADELEINE BARAN: Mahowald challenged the investigation. McDonough refused to let him see the investigative file. The case was closed. And once again, Mahowald was left feeling like the church had called him a liar. McDonough's hardball tactics worked. Mahowald never sued nor did most victims. McDonough and Flynn managed to contain the scandal. Victims stayed quiet. The names of priests stayed secret, and no one knew how big the cover-up really was.

REPORTER: This is MPR News Presents. You're listening to "Betrayed by Silence," the story of how three archbishops covered up child sexual abuse in the Archdiocese of Saint Paul and Minneapolis. And now, the conclusion of our special report is Madeleine Baran reports on the unraveling of the cover-up.

MADELEINE BARAN: Harry Flynn's time as archbishop was coming to a close in 2007. He was nearing 75, the mandatory retirement age for bishops. Pope Benedict named his replacement, conservative New Uhm bishop, John Nienstedt. Relations were chilly between the two men. Flynn chose to introduce his successor by reading off his credentials.

HARRY FLYNN: He has been a parish priest, a professor, a rector of a seminary, the pastor of a major national shrine, and an official at the Vatican. Secretary of State.

MADELEINE BARAN: Nienstedt brushed aside questions of ideology. He joked about his love of hockey and said parishioners should look to the Minnesota Wild to get a sense of his leadership style.

JOHN NIENSTEDT: I have seen them provide a solid, consistent play, a collaborative ethic of working as a team, and a determination to stick to the fundamentals of the game. Their style is one that I hope to emulate in my role as your coadjutor archbishop.

MADELEINE BARAN: Immediately, the tone at the chancery changed. Accounting director Scott Domeier.

SCOTT DOMEIER: Went from a friendly pastoral atmosphere to a very corporate and fearful environment.

MADELEINE BARAN: Nienstedt ruled by memo. No failing was too small to point out.

SCOTT DOMEIER: Why are there so many lights on overnight and on the weekends in the underground garage. You're wasting money.

MADELEINE BARAN: Domeier says chancery employees dreaded what they called "blue memo Mondays." Meanwhile, Nienstedt neglected more urgent concerns. The finances were so disorganized that Domeier was able to steal nearly $700,000 over years. He got caught in 2012 and sent to prison.

Nienstedt brought in his own team. He removed Father Kevin McDonough as the top deputy. For the first time in nearly two decades, McDonough was out of the inner circle. The archbishop hired an outsider to advise him on church law. Jennifer Haselberger shared Nienstedt's meticulous attention to detail, so much so that other senior officials found them grating. She also ran the records department, which gave her access to thousands of top secret memos and handwritten notes kept locked in the chancery vault.

JENNIFER HASELBERGER: The priest files were just, they were just an absolute mess.

MADELEINE BARAN: Incriminating documents on the sex crimes of priests had been removed. Haselberger found them stashed in boxes in the basement of the chancery. Her staff got to work merging the files so that when a priest came up for an assignment, the archbishop would have his complete history. It didn't take long for Haselberger to uncover a far worse problem. Several priests who had been accused of sexually abusing children were still in parishes, and the archdiocese wasn't following orders from the Vatican on how to handle them. The unraveling had begun.

That summer, a visiting priest from Ecuador had fled during a criminal investigation into whether he had sexually abused a four-year-old girl. No one had reported it to Rome. A chancery official told Haselberger he didn't know they were supposed to.

JENNIFER HASELBERGER: I mean, you could literally go to Google and say what to do when a priest has been accused of sexual abuse of a minor. And they would pull up. I mean, anybody could find it. And so the idea that they were unaware and that that hadn't been done just completely had me taken aback.

MADELEINE BARAN: Nienstedt would later claim that he had no idea his deputies weren't following the rules. But internal memos show that Haselberger warned Nienstedt during her first month on the job that the archdiocese was out of compliance with church law. When priests came up for assignment, Haselberger checked their files. Sometimes she found disturbing information, like with the case of Father Curtis Wehmeyer. His file showed a long history of sexual interest in young men. Haselberger alerted Nienstedt.

JENNIFER HASELBERGER: And I remember thinking at that time, all I have to do is tell him this and the argument is done.

MADELEINE BARAN: Nienstedt brushed off her concerns and kept Wehmeyer in ministry. Wehmeyer. Went on to sexually abuse two boys. He's now in prison. Haselberger also clashed with Nienstedt's top deputy, Vicar General Peter Laird.

JENNIFER HASELBERGER: And I remember one night in particular being after hours and me going to Father Laird's office with a file regarding a priest who I think the charter applied. And him turning around and actually looking at me and saying, do you think we have priests in ministry now that have sexually abused children? And I said, yes. And he just turned around and went back to typing at his computer.

MADELEINE BARAN: Haselberger kept digging. She found the secret financial deals that Flynn had made with abusers and told Nienstedt. But she wasn't getting much traction. She was just one voice among Nienstedt's top advisers, the lone woman. And she wasn't a priest. She argued with coworkers. And Laird suspended her in late 2012 because of a conflict with another employee. Near the end of Haselberger's time at the chancery, she saw a memo by accident from auxiliary bishop, Lee Piche.

JENNIFER HASELBERGER: Bishop Piche's memo talked about how I was belligerent on these matters. And at first, I was really hurt about that. That they would talk about me behind my back in this way and put in memos and things like that.

But then I got to thinking, I'm like, if staring in the face of abuse that could have been prevented wouldn't have prompted me to belligerently, if you want to use their term, argue for basic steps to protect children, then I would be very ashamed of myself.

MADELEINE BARAN: Haselberger resigned in protest in April 2013. In a resignation letter, she urged Nienstedt to publish the names of abusive priests and commission an independent review of clergy files. Nienstedt's reply was brief.

JENNIFER HASELBERGER: His letter said that he accepted my resignation and he had enjoyed working with me. And that was the extent of it.

MADELEINE BARAN: Nienstedt would soon face a change in the law, an aggressive attorney, and a whistleblower who knew all the secrets. Less than a month after Haselberger's resignation, the Minnesota legislature overcame decades of resistance from the Catholic Church and passed a law that gave victims whose cases had been shut out a chance to sue.

Victim's attorney Jeff Anderson, who'd spent decades gearing up for this moment, unleashed dozens of lawsuits. The archdiocese consulted with bankruptcy attorneys. And in July, Haselberger called MPR News. MPR aired its first investigative report on what the church knew about Father Curtis Wehmeyer in late September. Many Catholics responded with shock and anger.

Vicar General Peter Laird resigned within days. Nienstedt responded with promises of transparency. He convened a task force and hired a firm to review clergy files. A judge forced the archdiocese to do something victims groups had demanded for years-- disclose the names of abusive priests. Behind the scenes, the archbishop faced an uproar from his own priests over his role in the cover-up. A secret recording of an October meeting shows priests furious with their bishop.

PRIESTS: Archbishop, you're a liar, you're a thief, you're a coward.

MADELEINE BARAN: Over boos from his fellow priests, the man said he wasn't the only one who thought Nienstedt was a liar, a thief, and a coward. His parishioners called Nienstedt a liar because he knew about the problem and kept moving abusers around. A thief because he used church funds to cover it up. And a coward for hiding from the media for three weeks after the story broke.

In videotaped depositions, Anderson questioned Nienstedt and his predecessor, Harry Flynn, about the cover-up. Flynn professed little memory of abusers, answering he didn't know more than 130 times.

HARRY FLYNN: I was out of the diocese a great deal doing talks on the charter and trying to get diocese on board. And it's unfortunate that we did not pay more attention to this as a result.

MADELEINE BARAN: Anderson grilled Nienstedt on why he'd continued the cover-up.

JEFF ANDERSON: From 2008 until 2013, you made the choice to keep that list secret, did you not?

JOHN NIENSTEDT: It already had been kept secret, and I didn't see any reason to disclose.

MADELEINE BARAN: Some parishioners and priests have called for Nienstedt's resignation. A few have even written to the Pope. But parents like Cheryl and Jeff Herrity are pessimistic the church will change. It's been more than 30 years since their son was abused. Jeff Herrity says he's heard too many promises.

JEFF HERRITY: When you get these reports coming up that the church does it, oh, yeah, yeah, yeah. Then all of a sudden, two months from now, it's gone. And we're on to another subject, and nothing changed.

Still, children are out there getting abused. And then it would be another big thing they'll come up. And then they'll talk about it again. And then it'll go away again. And on and on and on. And until they're held up to somebody else's standards and are accountable, it isn't going to change.

MADELEINE BARAN: More than a decade ago, Catholic bishops vowed to change. Haselberger revealed the cover-up never ended. At the time she resigned in 2013, some accused priests were still in ministry. Despite all their public promises, church officials showed no interest in removing them.

JENNIFER HASELBERGER: The archdiocese is going to have to be called to account in a public forum in order for anything to change. And so, you know, my hope was that we'd have a grand jury or something similar that would really be able to shine a light on what's taken place.

MADELEINE BARAN: Ramsey County Attorney John Choi has refused to convene a grand jury. Nearly one year into the scandal, no one has faced criminal charges. Police have not asked the archdiocese to turn over all of its files.

Even today, the church is still refusing to disclose the names of every priest accused of sexually abusing a child. Nienstedt, Flynn, and other top officials have declined interview requests since September. Haselberger says, regardless of what happens in St. Paul, church leaders will eventually have to face what they've done.

JENNIFER HASELBERGER: As Catholics, even if it doesn't happen in this life, we know it will in the next. There'll be a reckoning.

[MUSIC PLAYING]

REPORTER: This is MPR News Presents. You can hear this special report again tonight at 9 o'clock in its entirety. And you can listen to it now or anytime online at mprnews.org. "Betrayed by Silence," a radio documentary was reported and produced by Madeleine Baran along with Sasha Aslanian, with help from Meg Martin, Tom Scheck, and Laura Yuen. It was edited by Mike Edgerly. Engineers were Erik Stromstad and Rob Byers. The project's editor is Chris Worthington.

Tomorrow at noon, more from the Aspen Ideas Festival. Up next on The Takeaway, a look at the escalating tensions between Israel and Hamas and whether a ceasefire can be reached. Plus, the Department of Justice has announced a $7 billion settlement with Citigroup.

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PHIL PICARDI: Baseball's best sluggers are in town for the All-Star Week's Home Run Derby tonight at Target Field. I'm Phil Picardi. A report on that event and all the latest news tomorrow on Morning Edition, weekdays, 4:00 to 9:00 AM, here on Minnesota Public Radio News.