The Roman Catholic Church is facing its biggest crisis in the United States since the Boston sex abuse scandal 16 years ago. 13 states are now investigating whether abuse was concealed by church leaders, including bishops who head each diocese. We have learned one place under scrutiny by federal investigators is Buffalo, New York. In August, information about dozens of accused priests was leaked from the diocesan secret archive. What it revealed, infuriated many of Buffalo's 600,000 Catholics. Tonight, you will hear from a priest who will share his direct knowledge about what he has called a cover-up. But first, the anonymous whistleblower who uncovered proof that Bishop Richard Malone withheld the names of dozens of priests accused of abuse.

"At the end of my life, I'm not going to answer to Bishop Malone. I'm going to answer to God."

Until now, Siobhan O'Connor had carefully kept her identity secret.

Siobhan O'Connor: I had to rely on God even more than I ever have before.

She is the whistleblower who leaked records from the secret archive of the Diocese of Buffalo. Siobhan O'Connor worked closely with Bishop Richard Malone as his executive assistant for three years. Last week she spoke with the FBI.

Correspondent Bill Whitaker with Siobhan O'Connor

Bill Whitaker: Some people would say that you betrayed Bishop Malone.

Siobhan O'Connor: I did betray him, and yet I can't apologize for that, because there was a greater good to consider.

The hundreds of pages Siobhan O'Connor uncovered included personnel files and memos. They revealed that for years Bishop Malone allowed priests accused of sexual assault such as statutory rape and groping to stay on the job.

Siobhan O'Connor: I love my church, I love our diocese, and I-- I loved him. I-- I genuinely did as my bishop and as my boss.

Bill Whitaker: So why are you doing this?

Siobhan O'Connor: The reality of what I saw really left me with no other option. Because at the end of my life, I'm not going to answer to Bishop Malone. I'm going to answer to God.

At first, she took pictures with her phone. Then she used the copy machine at the bishop's offices. The documents provided an extraordinary window into how the diocese handled abuse.

Bill Whitaker: And nobody caught on to what you were doing?

Siobhan O'Connor: No, they didn't. I was always working with paper, and I was always there, so it wasn't as though I had to ask for keys or take them from someone's desk.

Her decision to act was influenced by the phone calls she fielded from dozens of people who said they had been abused. O'Connor says she tried to get the bishop to be more responsive to them. He would tell her it's not her concern. She said by last summer she was, in her words, "morally allergic" to what she witnessed. Just before O'Connor quit her job in August, she anonymously leaked the church documents to a reporter at Buffalo television station WKBW.

Bill Whitaker: There was no other way you saw to handle this?

Siobhan O'Connor: Not with any expediency, no. I mean, I-- I did hope and pray that a grand jury would eventually be convened and that there would be hopefully an independent investigation, but I felt that there could be other victims between now and then, and I-- I couldn't have that on my conscience if there was a way to prevent that.

Bishop Richard Malone

Her doubts began in March. Bishop Malone had agreed to release a list of 42 priests accused of sexually abusing minors. But O'Connor knew there should be more names because she had seen the draft list that circulated between the bishop and diocesan lawyers. There was also something else, a dossier about priests she discovered in a supply closet.

Siobhan O'Connor: There was one particular binder, which was of pending litigation that had been presented to Bishop Malone when he first was installed as our bishop. And this was from the lawyers. And this was a large, over 300-page binder, and I found it when I was cleaning the closet where they kept the bishop's vacuum. And I remember finding this obviously very important and sensitive information and thinking, "How did it ever end up here, first of all?" And-- and then I was shocked at the volume of it.

The cases in the dossier Bishop Malone inherited when he arrived in 2012 stretched back decades. As they worked on the list, the bishop and his lawyers decided they would not reveal the names of accused priests still in ministry.

Siobhan O'Connor: It was a very carefully curated list. And I-- I saw all the-- the lawyers coming in and out, and I was aware of the-- the various strategies that were in place.

Bill Whitaker: What were they trying to do if not help the victims?

Siobhan O'Connor: Well, to my mind the overarching attitude seemed to be to protect the church's reputation and her assets.

Bill Whitaker: And the assets?

Siobhan O'Connor: Uh-huh. Very much so.

Siobhan O'Connor was most alarmed to see that Father Arthur Smith was missing from the list. Church records showed two young men in Buffalo had complained in 2013 that Smith had inappropriately touched them. Two years before that, Smith was sent to counseling after repeated contact with an eighth-grade boy that included unwanted attention and facebook messages. Despite what Bishop Malone knew, he endorsed Smith for a job as a cruise ship chaplain. The bishop wrote, "I am unaware of anything in his background which would render him unsuitable to work with minor children".

Siobhan O'Connor: Our previous bishop had removed him from ministry, so I always thought it was odd that Bishop Malone had reinstated him. When I explored his file more in-depth, that might have really been the moment when I knew that I had to do something with this information.

Remember, the diocese list had 42 names. The documents O'Connor revealed put the number of Buffalo priests facing claims of all types of abuse at 118.

Bill Whitaker: They had accusations against them, credible accusations.

Siobhan O'Connor: Yes, that's right.

Bill Whitaker: What'd you think of that?

Siobhan O'Connor: I felt that instead of being transparent, we were almost being the opposite or-- or half transparent. Here are the names that we would like you to know about, but please don't ask us about the rest.

One of them was Father Fabian Maryanski. His file included an accusation that during the 1980's he had sexual relations with a girl that began when she was just 15. The diocese knew about it but a note in the file argued Maryanski should be excluded from the list of problem priests. It said, "We did not remove him from ministry despite full knowledge of the case, and so including him on list might require explanation."

Siobhan O'Connor: And I remember thinking, if that's their rationale for leaving a priest off, then how can I abide by this?

She was not alone. Father Bob Zilliox advised the bishop on church law, including abuse cases. He told us he was disgusted by how the cases he saw were handled.

Father Bob Zilliox

Father Bob Zilliox: I think the hypocrisy, the lip service, you know, the, "Yes, Bob, I agree with you," and then I would walk out of an office and nothing would happen.

It is exceedingly rare for a Catholic priest to risk challenging his bishop in public. Father Zilliox left his role as the bishop's counsel in May to concentrate on his parish ministry.

Father Bob Zilliox: A lot of cases should have been handled differently. They were not. A lot of cases probably should have gone to Rome at the time. They did not.

Bill Whitaker: How many of those priests should have been taken out of priesthood?

Father Bob Zilliox: I would argue at least eight or nine.

Bill Whitaker: How many of them still are in the priesthood here in Buffalo?

Father Bob Zilliox: All of them.

Bill Whitaker: All of them?

Father Bob Zilliox: All the guys that should have been removed from the priesthood are still priests.

Bill Whitaker: What do you think of that?

Father Bob Zilliox: It's beyond troubling. That's not the church. The church is holy. Those are individuals in the church who are weak and who have made very bad decisions. And because of that, they need to be held accountable for what they've done.

Bill Whitaker: Why is it, do you think, that the clergy fails to get this?

Father Bob Zilliox: I think one of the factors that goes into decision making in terms of administration or leadership within diocese or in parishes is that there's a certain brotherhood. There's a certain mindset that we watch each other's backs.

Bishop Malone has the authority to strip Father Zilliox of his duties for going public. But the priest told us he is motivated to speak out by more than the truth. He also is a victim of sexual abuse by a Buffalo priest.

Father Bob Zilliox: And so all of this has been very painful for me to see how our diocese, how other dioceses have handled this.

Bill Whitaker: How old were you when you were abused?

Father Bob Zilliox: I was a 13-year-old boy.

Bill Whitaker: By a priest?

Father Bob Zilliox: By a priest.

Bill Whitaker: How did that experience affect you while you were watching how Bishop Malone was handling these cases?

Father Bob Zilliox: It was very difficult in a lot of different ways. There's a certain respect that is owed to a bishop. But when I saw things take place the way they did, I sort of was conflicted within. I think as a victim, I have a bias, which is maybe not a healthy thing, but objectively I can-- I have no tolerance for any abuse.

"I want these cardinals and bishops to start putting their ass on the line and start protecting their people."

Every bishop chooses a motto. Bishop Malone's is 'live the truth in love.' Bishop Malone declined our requests for an interview.

Paul Snyder: He's behaving in a way that you would typically think that a CEO in a corporation that's being accused of corrupt practices might act, hiding behind attorneys.

Paul Snyder was the first member of Buffalo's Catholic clergy to call for Malone to resign. The hotel owner is a deacon, that's an ordained member of the clergy who can be married and preside over some ceremonies. He was enraged by the information Siobhan O'Connor exposed.

Paul Snyder

Bill Whitaker: Bishop Malone has called this a crisis. You call it a scandal. What's the difference?

Paul Snyder: A crisis is we look at our home and it's burning to the ground. A scandal is while it's burning to the ground, you know how to put the fire out, but you don't tell me. You also know how the fire was caused, but you don't tell me. So you pretend to grieve with me about the fire, but the problem is you caused it.

Snyder showed us some of the 400 notes and emails he has received since calling for the bishop to resign.

Paul Snyder: They want to be part of the solution but they think this bishop is preventing that from occurring.

This month, Snyder sent letters and documents to prominent bishops demanding an investigation.

Bill Whitaker: Why do you have faith that the bishops are going to handle this?

Paul Snyder: Well, I don't have faith right now that any particular bishops have the courage to do the right thing. I mean we all praise our martyrs on Sunday and we praise and we sing, but boy, its sure as hell is hard being a saint when it's your ass on the line. And I want these cardinals and bishops to start putting their ass on the line and start protecting their people.

Bishops hold supreme power in their diocese and answer only to the pope. Next month, U.S. bishops will gather to consider a proposal for a bishop code of conduct. Bishop Malone plans to be there. He's refused to resign.

Bishop Malone at August Press Conference: The shepherd does not desert the flock at a difficult time.

The bishop has made three public apologies and offered to sell his 11,000 square foot official residence to help compensate victims.

Last week, he sent us a statement that said in part: "We continue to reach out to victims, remove clergy with substantiated allegations from ministry and cooperate with federal and state investigations."

But in Bishop Malone's first six years in Buffalo just one priest was put on leave. It was only after this scandal broke in March, that he suspended 16 more for abuse. None have been kicked out of the priesthood.

Bill Whitaker: He has said he is sorry. He has apologized.

Father Bob Zilliox: Uh-huh.

Bill Whitaker: Do you forgive him?

Father Bob Zilliox: I accept it and I forgive him, but actions speak louder than words. Show us these cases are being handled properly. Show us these priests are being removed.

Bill Whitaker: You would like for Bishop Malone to resign?

Siobhan O'Connor: I would. I-- I believe that it would be in the best interest of the diocese, because he's had opportunities to enact real change. And he's let those opportunities come and go.

Produced by Guy Campanile and Lucy Boyd. Associate producer, Dina Zingaro.