The Catholic Church's Secret Sex-Crime Files

How a scandal in Philadelphia exposed documents that reveal a high-level conspiracy to cover up decades of sexual abuse

cardinal bevilacqua archbishop philadelphia sex scandal
William Thomas Cain/Getty Images
Cardinal Anthony Bevilacqua, the former Archbishop of Philadelphia, was involved in the cover-up of multiple incidents of sexual abuse.
By |

The five co-defendants sit close enough to shake hands in the Philadelphia courtroom, but they never once acknowledge one another. Father James Brennan, a 47-year-old priest accused of raping a 14-year-old boy, looks sad and stooped in a navy sweater, unshaven and sniffling. Edward Avery, a defrocked priest in his sixties, wears an unsettlingly pleasant expression on his face, as though he's mentally very far away. He and two other defendants – the Rev. Charles Engelhardt, also in his sixties, and Bernard Shero, a former Catholic schoolteacher in his forties – are accused of passing around "Billy," a fifth-grade altar boy. According to the charges, the three men raped and sodomized the 10-year-old, sometimes making him perform stripteases or getting him drunk on sacramental wine after Mass.

Heinous as the accusations are, the most shocking – and significant – are those against the fifth defendant, Monsignor William Lynn. At 60, Lynn is portly and dignified, his thin lips pressed together and his double chin held high. In a dramatic fashion statement, he alone has chosen to wear his black clerical garb today, a startling reminder that this is a priest on trial, a revered representative of the Catholic Church, not to mention a high-ranking official in Philadelphia's archdiocese. Lynn, who reported directly to the cardinal, was the trusted custodian of a trove of documents known in the church as the "Secret Archives files." The files prove what many have long suspected: that officials in the upper echelons of the church not only tolerated the widespread sexual abuse of children by priests but conspired to hide the crimes and silence the victims. Lynn is accused of having been the archdiocese's sex-abuse fixer, the man who covered up for its priests. Incredibly, after a scandal that has rocked the church for a generation, he is the first Catholic official ever criminally charged for the cover-up.

"All rise," the court crier intones as the judge enters, and Lynn stands, flanked by his high-powered lawyers, whose hefty fees are being paid by the archdiocese. The implications of the trial are staggering for the church as a whole. In sheltering abusive priests, Lynn wasn't some lone wolf with monstrous sexual appetites, as the church has taken to portraying priests who have molested children. According to two scathing grand-jury reports, protocols for protecting rapists in the clergy have been in place in Philadelphia for half a century, under the regimes of three different cardinals. Lynn was simply a company man, a faithful bureaucrat who did his job exceedingly well. His actions were encouraged by his superiors, who in turn received orders from their superiors – an unbroken chain of command stretching all the way to Rome. In bringing conspiracy charges against Lynn, the Philadelphia district attorney is making a bold statement: that the Catholic hierarchy's failure to protect children from sexual abuse isn't the fault of an inept medieval bureaucracy, but rather the deliberate and criminal work of a cold and calculating organization. In a very real sense, it's not just Lynn who is on trial here. It's the Catholic Church itself.

The deluge of sexual-abuse cases in America's largest religious denomination began in 1985, when a Louisiana priest was sentenced to 20 years in prison after admitting to sexually abusing 37 boys. But it wasn't until 2002, when civil suits in Boston revealed that Cardinal Bernard Law had shielded rapist priests, that the extent of the scandal became widely known. In Germany, the church is overwhelmed by hundreds of alleged victims, and investigations are under way in Austria and the Netherlands. In Ireland, the government recently issued a scathing report that documents how Irish clergy – with tacit approval from the Vatican – covered up the sexual abuse of children as recently as 2009.

Battered by civil suits and bad press, the church has responded with a head-spinning mix of contrition and deflection, blaming anti-Catholic bias and the church's enemies for paying undue attention to the crisis. The U.S. Conference of Catholic Bishops helped fund a $1.8 million study of sex-abuse cases against priests, but the results read like a mirthless joke: To lower the number of clergy classified as "pedophiles," the report redefines "puberty" as beginning at age 10 – and then partially blames the rise in child molesting on the counterculture of the 1960s. The church also insists that any sex crimes by priests are a thing of the past. "The abuse crisis," the study's lead author concluded, "is over."

That echoed statements by Archbishop Timothy Dolan of New York, who went on 60 Minutes declaring the scandal "nothing less than hideous" and then, with a sweep of his hand, announced, "That's over with!" Dolan, in turn, sounded a lot like Bishop Wilton Gregory, the former president of the USCCB, who framed the lie more eloquently: "The terrible history recorded here is history." That was in 2004, seven years ago.

Given how the innermost workings of Catholic culture have long been cloaked in secrecy, the case in Philadelphia offers a rare opportunity to understand why the cover-up of sexual abuse has continued for so long, despite the church's repeated promises of reform. The answer, in large part, lies in the mindset of the church's rigid hierarchy, which promotes officials who are willing to do virtually anything they're told, so long as it's in God's name. "It's almost like the type of stuff you see in cult behavior," says a former Philadelphia priest who asked not to be identified for fear of retribution. "Someone on the outside would say, 'That's crazy.' But when you're on the inside, you say, 'It's perfectly right, because everything is divinely inspired.' If you have a monopoly on God, you can get away with anything."

Long before he became the guardian of the church's secrets, Bill Lynn was a boy with a higher calling. In the fall of 1968, after graduating from Bishop McDevitt High School in the suburbs of Philadelphia, Lynn arrived at St. Charles Borromeo Seminary, a stately campus whose soaring chapels, somber libraries and marble sculptures with heads bowed in prayer gave off an aura of reverence, history and costly precision. Lynn, a friendly, overweight boy whose acne-scarred face was topped with jet-black hair, was ready to begin his eight-year path to priestly ordination, a process the church calls "formation."

At St. Charles, Lynn was plunged into an environment in which every moment was accounted for. Strict rules governed all aspects of life, especially the personal. Besides the obvious prohibitions on sexual contact – including with oneself, or even in one's imagination – no seminarian was allowed to get too close with his peers, since he was to concentrate on developing bonds with God and the church. Seminary is a form of military-style indoctrination, molding men to think institutionally, not individually. "It's like a brainwashing, almost," says Michael Lynch, who attended St. Charles for nine years but was rejected for priesthood after repeatedly butting heads with his superiors. Lynch recalls a priest barking at his class, "We own you! We own your body, we own your soul!"

The goal of priesthood is a lofty one: a man placed on a pedestal for his community to revere, an alter Christus – "another Christ" – who can literally channel the power of Jesus and help create the perfect society intended by God. To model that perfection and elevate themselves above the sinful laity, clergy adopt a vow of celibacy, which has served as a centerpiece of Catholic priesthood since the 12th century. It's a tall order to sculpt chaste, living incarnations of Jesus out of the sloppy clay of your average 18-year-old male. Even many of those who wind up being ordained fail to maintain their chastity: According to a 1990 study by psychologist Richard Sipe, only half of all priests adhere to their vows of celibacy. It is not just the sex-abuse epidemic the church seeks to deny, but sex itself.

"The real secret here is the sexual life of cardinals and bishops," says Sipe, a former Benedictine monk who specializes in treating clergy and who has followed the case against Lynn. "If you pull the string in a knitted sweater, you'll unravel the whole thing. This will unravel all the way to Rome."

Many seminarians dropped out of St. Charles; others, informed that they weren't priestly material, were "invited" to leave. Those who remained were the ones willing to surrender to the process of formation: men prepared to bend to the will of their higher powers, both earthly and divine. Such intensive focus on preparing for one's "priestly burdens," however, often meant that men emerged from the incubator of seminary ill-prepared for the complexities of life itself. In 1972, while Lynn was still at St. Charles, a landmark study called "The Catholic Priest in the United States: Psychological Investigations" found that three-fourths of all American priests were psychologically and emotionally underdeveloped, or even "maldeveloped." The attitudes of these grown men toward sex, the study concluded, were on par with those of teenagers or even preteens.

Lynn thrived in seminary, where he made an impression as an affable guy who always toed the line. At his ordination, he took a solemn oath of obedience to the bishop, sealing himself into the church's vertical framework, in which everyone is bound to the strata above them. He was assigned first to a parish in Philadelphia, then to a wealthy church in the suburbs. His parishioners liked him, and Lynn's deference to his senior pastor made an impression on the archdiocese. In 1984, when a job as dean of men opened up at St. Charles, Lynn was plucked to fill it. "The dean is there to make sure you're being formed properly," explains a former Philadelphia priest familiar with the appointment. "A dean is also the type of person you want your students to want to be. We wanted to replicate priests in the model we had already been creating – nice, compliant, faithful priests. So we put Bill Lynn there: a nice, compliant, faithful priest we wanted young men to look up to."

Over the next eight years, Lynn was a hands-on adviser. He'd wake seminarians who overslept for Mass, take them to task for missing household chores and monitor their spiritual progress. Lynn proved himself to his superiors as someone who didn't disrupt the status quo, someone who could be trusted. In 1992, at age 41, he was named secretary of the clergy, a position that effectively made him the human-resources director for the 400 or so priests in greater Philadelphia. It was a job that required the utmost loyalty and discretion. Lynn now reported directly to Cardinal Anthony Bevilacqua. If a priest broke the rules or stepped out of line in any way, it would be Lynn's job to discipline him and inform his superiors. That, says the former priest familiar with St. Charles, is precisely why Lynn was chosen for the job: "They sure as hell weren't going to pick someone who was going to send priests to jail."

Every Catholic diocese has Secret Archives files – it's mandated by canon law as a repository for complaints against priests so scandalous that they must be kept out of the regular personnel files. Few outsiders know the secret archives exist, and only the most trusted clergy have access to them. In Philadelphia, the sole keyholders were the cardinal and his closest aides. The files were kept in a row of unlabeled, gray-green cabinets in a windowless room on the 12th floor of the archdiocese's Center City office tower. Inside was an exhaustive compendium of scandals dating back more than 50 years: priests with drinking problems, priests who had gotten women pregnant, aging stacks of confiscated pornography. Then there were the reams of carefully typed memos that discussed priests with what the archdiocese delicately referred to as "unnatural involvements" or "unusual patterns." Priests, in other words, who had sexually abused the children in their care.

One memo directed to Cardinal Bevilacqua in 1989 described a pedophile priest's evaluation at an archdiocese-owned hospital, in which the doctor "is of the very strong opinion that Father Peter J. Dunne is a very sick man" who should be removed from ministry; the memo warned that Dunne's problem was so acute "that we are sitting on a powder keg." Another file began with a sheaf of letters that Father Joseph Gausch, an active pastor, had sent another priest detailing his sex with an eighth-grade boy in 1948, three years after his ordination. Gausch called it "the closest approximation to an old-fashioned roll that I have had in years... and the subject was oh-so-satisfactory and (this is what makes the story) willin'." In both cases, the response from the cardinal was the same: secret therapy, then reassign the offending priest to a new parish and pretend nothing had happened.

In the thick file devoted to Father Raymond Leneweaver, who had been moved to four different parishes after admitting to molesting at least seven boys, officials fretted in 1980 that they had run out of places to send him "where his scandalous action would not be known." Scandal is a word that pops up throughout the Secret Archives files. The officials writing the internal memos almost never express concern for the victims – only concern over the risk to the church's reputation. If the risk was deemed low, an offending priest was simply reassigned to a different parish. If the risk was high, priests were shipped to a far-off diocese with the permission of the reigning bishop, a practice known as "bishops helping bishops."

Even in rare cases where word of a priest's crimes leaked out, the cardinal was reluctant to expose the priest. Leneweaver was such a case; his ministry career ended only after he resigned. "His problem is not occupational or geographical," wrote the cardinal at the time, "and will follow him wherever he goes." Having acknowledged the severity of Leneweaver's compulsions, the cardinal released him from the clergy but still chose not to inform law-enforcement officials of his crimes. With his clean record, Leneweaver, an admitted child-rapist, went on to take a job as a teacher at a public middle school in suburban Philadelphia.

Bill Lynn understood that his mission, above all, was to preserve the reputation of the church. The unspoken rule was clear: Never call the police. Not long after his promotion, Lynn and a colleague held a meeting with Rev. Michael McCarthy, who had been accused of sexually abusing boys, informing the priest of the fate that Cardinal Bevilacqua had approved: McCarthy would be reassigned to a "distant" parish "so that the profile can be as low as possible and not attract attention from the complainant." Lynn dutifully filed his memo of the meeting in the Secret Archives, where it would sit for the next decade.

Over the 12 years that he held the job of secretary of the clergy, Lynn mastered the art of damage control. With his fellow priests, Lynn was unfailingly sympathetic; in a meeting with one distraught pastor who had just admitted to abusing boys, Lynn comforted the clergyman by suggesting that his 11-year-old victim had "seduced" him. With victims, Lynn was smooth and reassuring, promising to take their allegations seriously while doing nothing to punish their abusers. Kathy Jordan, who told Lynn in 2002 that she had been assaulted by a priest as a student at a Catholic high school, recalls how he assured her that the offender would no longer be allowed to work as a pastor. Years later, while reading the priest's obituary, Jordan says it became clear to her that her abuser had, in fact, remained a priest, serving Mass in Maryland. "I came to realize that by having this friendly, confiding way, Lynn had neutralized me," she says. "He handled me brilliantly."

In his very first year on the job, Lynn received a letter from a 29-year-old medical student that would trigger the events that led to his arrest 19 years later. The student – whom the grand jury would call "James" – reported that as a teenage altar boy he had been molested by his priest, Father Edward Avery. The popular and gregarious Avery, nicknamed "The Smiling Padre," was considered hip for a priest; he moonlighted as a DJ at weddings and invited lucky boys for sleepovers at his house at the Jersey Shore. The med student included a copy of a letter he had written to Avery. "I have let too much of my life be controlled by this terrible wrong you committed," it read. "You had no right to hurt me the way you did. You have no right to hurt anyone else this way."

This was a code-red situation that Lynn had to get under control. He began by interviewing James, who described how Avery had molested him at the beach house, at the parish rectory and on a ski trip to Vermont, sometimes after plying him with beer. James said he wasn't looking for money – only an assurance that Avery would no longer be a threat to children. That was surely a relief: the risk of scandal was clearly low. Next, Lynn confronted Avery, whom he'd known in seminary. According to Lynn's memo, the priest admitted that some of the allegations "could be" true – but insisted it had been "strictly accidental" and that he had been so drunk at the time, he couldn't recall exactly what had happened.

According to church protocol, an admission of any kind meant a priest must be sent for medical care. So Lynn recommended that Avery seek treatment at St. John Vianney Hospital, a facility in the leafy Philadelphia suburb of Downingtown that maintained a discreet inpatient program that treats sexually abusive priests. Cardinal Bevilacqua approved the request, but the bureaucratic wheels moved slowly: Avery remained in the pulpit for another 10 months before he was hospitalized for his secret therapy. After his release, his doctors prescribed that he be monitored by an aftercare team consisting of Lynn and two other priests. But the church did not take the recommendation seriously. The team did not meet for more than a year – one priest later testified that he didn't even know he was on the team.

Avery's doctors also recommended that he be kept away from teens and other "vulnerable" populations. Instead, the church assigned Avery to a new residence with plenty of exposure to kids: St. Jerome, a parish in northeast Philadelphia that included an elementary school. (The rectory had an empty bed because its previous resident, Rev. Bill Dougherty, had been quietly moved to another parish after being accused of abusing a high school girl.) Officially speaking, Avery didn't work at the parish – he simply lived there, with an assignment as a chaplain at a nearby hospital. With encouragement from Lynn, he became a regular presence at St. Jerome, serving Mass and hearing confessions. He took on more DJ jobs than ever, booking gigs almost every weekend. "He seemed mesmerized, focused, as if he became a different person DJ'ing," recalls Rev. Michael Kerper, who split shifts with Avery at the hospital. Kerper, under the impression that Avery had been moved to a low-pressure chaplain job after a nervous breakdown, worried that Avery was risking another collapse by spreading himself so thin. One day, when Avery failed to show up at the hospital while on call, Kerper wrote the archdiocese to express his concern. He addressed his letter to Monsignor Lynn.

Lynn surprised Kerper by calling him directly and telling him to mind his own business. "You're not going through the proper channels," Lynn snapped. "You're not his supervisor." Avery was permitted to continue working as a DJ and pitching in at St. Jerome. The following year, according to the grand jury, Lynn received an ­e-mail from James, who was looking for assurance that Avery had been reassigned to "a situation where he can't harm others... for my peace of mind, I have to know." Lynn reassured James that the archdiocese had taken proper steps. Then Lynn met with Avery and instructed him to be "more low-keyed." In doing so, says the grand jury, Lynn helped set the stage for the horror that came next.

"Billy" was a 10-year-old student at St. Jerome School in 1998, and an altar boy just like his older brother before him. A sweet, gentle kid with boyish good looks, Billy was outgoing and well-liked. One morning, after serving Mass, Rev. Charles Engelhardt caught Billy in the church sacristy sipping leftover wine. Rather than get mad, however, the priest poured Billy more wine. According to the grand jury, he also showed him some pornographic magazines, asking the boy how the pictures made him feel and whether he preferred the images of naked men or women. He told Billy it was time to become a man and that they would soon begin their "sessions."

A week later, Billy learned what Engelhardt meant. After Mass, the priest allegedly fondled the boy, sucked his penis and ordered Billy to kneel and fellate him – calling him "son" while instructing him to move his head faster or slower – until Engelhardt ejaculated. The priest later suggested another "session," but Billy refused and Engelhardt let him be.

A few months later, while Billy was putting away the bells following choir practice, he was taken aside by another priest: Father Avery. According to the grand jury, Avery told Billy that he had heard all about the boy's "session" with Engelhardt – and that Avery's own "sessions" with him would soon begin. Billy pretended not to know what Avery was talking about, but his stomach lurched. Later, after Billy served a morning Mass with Avery, the priest led him to the sacristy, turned on some music and told him to do a striptease. When Billy dutifully started shedding his clothes, Avery instructed him to dance to the music while undressing. Then the Smiling Padre sat back and watched the awkward performance before taking off his own clothes and ordering the naked boy onto his lap. He kissed Billy's neck and back, telling him that God loved him. Then he allegedly fondled the boy, fellated him, and commanded Billy to return the favor, culminating in Avery's ejaculating on Billy and congratulating him on a good "session." A second session allegedly followed weeks later when Avery, finding Billy cleaning a chalice after a weekend Mass, ordered the boy to strip. The priest then fellated Billy while making the boy masturbate him to climax.

Billy never told anyone what had happened. But from then on, he made sure to trade assignments with other altar boys to avoid serving Mass with Father Avery. After summer break, when Billy returned to St. Jerome and entered the sixth grade, he was assigned a new teacher, Bernard Shero. His abuse seemed to be a thing of the past, something best forgotten.

One day, according to the grand jury, Shero offered Billy a ride after school. Instead, they stopped at a park about a mile from Billy's house. "We're going to have some fun," Shero told him. He ordered Billy into the back seat, helped him undress, and then allegedly fellated and anally raped him, managing to insert his penis only partway because of Billy's screams of pain. Then Shero made Billy perform the same acts on him. "It feels good," he repeated over and over. Afterward, he made Billy get out of the car and walk home.

Before long, Billy began to change in disturbing ways. He often gagged or vomited for no reason and became increasingly sullen and withdrawn. He stopped hanging out with his friends and playing sports. He started smoking pot at 11; by his late teens, he was addicted to heroin. Billy spent his adolescence cycling in and out of drug-treatment programs and psychiatric centers, once spending a week in a locked ward after a suicide attempt. His parents, who later took out a mortgage on their home to pay for Billy's care, were beside themselves, clueless as to what had sent their sunny child into such a downward spiral.

When his mother found two books about sexual abuse stashed under his bed, Billy brushed off her suspicions. The books were for an assignment at school, he told her, and refused to say anything more.

Billy's alleged abuse at the hands of the Philadelphia priests might have remained a secret, if not for the church's inept attempt at spin control. After the abuse scandal in Boston broke open in 2002, every Catholic diocese in America had rushed to reassure its parishioners. Philadelphia was no different: Cardinal Bevilacqua declared that in the previous 50 years, his archdiocese knew of only 35 priests who had been credibly accused of sexual abuse. That was news to Lynne Abraham, the city's district attorney at the time, since not a single one of those 35 cases had been reported to her office. When Abraham asked the archdiocese's law firm for details, it refused to cooperate. In the face of stonewalling, Abraham moved for a grand-jury investigation and assigned a team of prosecutors nicknamed "The God Squad" to probe the archdiocese's handling of sex-abuse claims.

The God Squad had no idea what they were in for. The archdiocese fought the investigation at every turn. "It was like trying to infiltrate a racketeering organization," recalls former Assistant District Attorney Will Spade. "Most of these guys just seemed to be in the wrong professions. They weren't kind or understanding or any of the things a priest should be. They were just thugs."

The grand jury subpoenaed the church's internal records. Compelled by the court, the church's lawyer began meeting with prosecutors at a Dunkin' Donuts midway between the archdiocese's headquarters and the DA's office, handing over the ­Secret Archives files piece by piece. "I felt like I was living in a detective novel," says Spade. Though the prosecutors had been anticipating some sort of internal records, they were taken aback at the very existence of the secret files. "I always thought it was funny, them calling it the Secret Archives files," he says. "You morons! If they're so secret, why are you even calling it that?"

When the secret archives were finally unlocked, prosecutors were stunned to find thousands of documents that detailed the hundreds of victims who had allegedly been abused by 169 priests. "There was so much material, we could still be presenting information to the grand jury today if we followed every lead," says Charles Gallagher, a former Philadelphia deputy district attorney who supervised the investigation. "We ultimately had to focus."

In 2005, the grand jury released its 418-page report, which stands as the most blistering and comprehensive account ever issued on the church's institutional cover-up of sexual abuse. It named 63 priests who, despite credible accusations of abuse, had been hidden under the direction of Cardinal Bevilacqua and his predecessor, Cardinal Krol. It also gave numerous examples of Lynn covering up crimes at the bidding of his boss.

In the case of Rev. Stanley Gana, accused of "countless" child molestations, Lynn spent months ruthlessly investigating the personal life of one of the priest's victims, whom Gana had allegedly begun raping at age 13. Lynn later helpfully explained to the victim that the priest slept with women as well as children. "You see," he said, "he's not a pure pedophile" – which was why Gana remained in the ministry with the cardinal's blessing.

Then there was Monsignor John Gillespie, who was not sent for medical evaluation until six years after Lynn began receiving complaints about him. Therapists subsequently reported that Gillespie was "dangerous" – but Lynn was more concerned about the priest's insistence on apologizing to his victims. To keep the scandal from becoming public, Gillespie was ordered to resign for "health reasons." Cardinal Bevilacqua then honored the priest with the title of pastor emeritus – and allowed him to hear the confessions of schoolchildren for another year.

"In its callous, calculating manner, the archdiocese's 'handling' of the abuse scandal was at least as immoral as the abuse itself," the grand jury concluded. Immoral didn't mean illegal, however, and the grand jury found itself unable to recommend any prosecutions, in part because the statute of limitations on all of the abuse cases had run out. But the nightmare had been revealed, and the Philadelphia faithful recoiled in shock.

Perhaps no one was more disturbed than the new parishioners of Lynn, who had been quietly reassigned to a plum job as pastor of St. Joseph's, a rich suburban parish. The job was essentially a promotion: Lynn's predecessor had just been ordained a bishop and given a diocese of his own. A kind and jocular pastor, Lynn had swiftly become beloved in the parish, always happy to pitch in at events held by the Home & School Association or to host dinner parties in his rectory. Stunned by the grand-jury report, parishioners were at a loss to square the unfeeling church official who had manipulated innocent victims with the compassionate pastor whom they knew. In the rectory dining room, one woman confronted Lynn in tears.

"How did you do this?" she demanded, sobbing. "Why did you do this?"

Lynn looked her right in the eye. "Don't believe everything you read," he said firmly. "I put them in treatment. I took care of the families."

The first of the 63 priests listed in the grand jury's catalog of abusers was Father Avery. By then, Avery had been placed on administrative leave – but he still remained in the ministry, more than a dozen years after the allegations of sexual abuse against him had first surfaced.

Once again, it was the most powerful word in the secret archives – scandal – that spurred the church to take action. As the grand jury was preparing to release its report, Cardinal Justin Rigali "urgently" petitioned Rome to take the extreme step of defrocking Avery against his will. "There is a great danger of additional public scandal so long as Father Avery remains a cleric," he wrote, explaining that accusations against Avery had been in the papers and that his files had been subpoenaed. The Vatican needed to remove Avery from the priestly rolls, the cardinal urged, to avoid "additional scrutiny."

Rigali needn't have worried. According to the grand jury, Avery was persuaded to request a voluntary defrocking, thanks to a severance payment of $87,000. The laicization process of transforming a priest back into an ordinary civilian, which usually takes years of canonical trials, was completed in less than six months.

With Avery disposed of, Cardinal Rigali went about calming Philadelphia Catholics. The archdiocese retained a consultant to help it improve the handling of victim complaints. A centerpiece of the reform was an independent clergy-review board that evaluated accusations of abuse. It was a terrific idea, one that would inject transparency and accountability into the process by taking cases out of the shadowy archdiocese and putting them into the unbiased hands of others. In practice, however, the archdiocese simply cherry-picked cases to send to the board – a fact that board members themselves learned only after the secrecy was revealed by the grand jury last February. "The board was under the impression that we were reviewing every abuse allegation received by the archdiocese," board chair Ana Maria Cantazaro complained in an essay for the Catholic magazine Commonweal.

In the few cases that were actually submitted to the panel, the grand jury found that "the results have often been worse than no decision at all." Using lax standards developed in large part by the canonical lawyers, the board dismissed even highly credible allegations. The results of those decisions could be devastating. In 2007, a man named Daniel Neill complained that he had been abused as an altar boy by Rev. Joseph Gallagher. According to a lawsuit filed against the archdiocese, Neill gave three statements to an archdiocese investigator – only to be informed that the review board didn't believe him. Devastated, Neill killed himself in 2009. After the grand-jury report, the archdiocese finally reversed itself by suspending Gallagher.

Under another reform instituted by the archdiocese – the Victim Assistance Program – abuse survivors like Neill could receive counseling paid for by the church. "I urge anyone who was abused in the past to contact our Victim Assistance Coordinators, who can help begin the healing process," Cardinal Rigali declared. In reality, the grand jury found, the program was used as a way to discourage victims from calling the police and, even more insidiously, to extract information that could later be used against the victim in court. In a recent lawsuit against the archdiocese, one victim recounts how, in return for any assistance, the church pressured him to sign an agreement that "prohibited" the archdiocese from reporting the abuse to law enforcement. "All along, they were acting like they wanted to help me," says the victim, "but really they just wanted to help themselves."

When Billy, the altar boy allegedly passed around by Avery and others, sought help in 2009, the archdiocese's victim coordinators once again took measures to protect the church. Instead of immediately offering to take the case to the police, the grand jury found, a coordinator named Louise Hagner and another staffer showed up at Billy's house, where they pressured him into giving a graphic statement. Returning to her office, Hagner wrote up her notes – including her observation that she thought Billy had pretended to cry – and informed the church's lawyers that Billy intended to sue.

At least one good thing came out of Billy's case: When his allegations were finally brought to the district attorney's office, his case, which falls within the statute of limitations for criminal prosecution, became the foundation of the grand jury's current investigation. Even the Vatican itself appeared to take drastic action: On September 8th, Cardinal Rigali will be replaced by Charles Chaput, the charismatic archbishop of Denver. The Vatican insists, however, that Rigali's resignation has nothing to do with the scandal. Indeed, Pope Benedict XVI has shown nothing but support: In April, when the pontiff needed a special envoy to appear on his behalf in the Czech Republic, he chose none other than Rigali for the honor.

As for Cardinal Bevilacqua, under whose watch Billy and other children were allegedly abused, the grand jury regretfully noted that it could not recommend criminal charges in the current case, since it lacked direct evidence against the cardinal. Bevilacqua, now 88, has rejected responsibility for the abuses that occurred during his tenure. When he testified before the grand jury in 2003, Bevilacqua conceded that any move involving the reassignment of accused priests was "ultimately my decision." But he was quick to stress who was really at fault: In every instance, he insisted, he had "relied on my secretary of the clergy's recommendations if anything was necessary to be done." With Bevilacqua insulated from prosecution, the district attorney grabbed at a lower-level bureaucrat, one the cardinal himself had hung out to dry: Monsignor Bill Lynn.

Lynn stands in the courtroom in Philadelphia, having been sworn in by Judge Renée Cardwell Hughes. Hands clasped, his face pulled into a frown of concentration, the monsignor proceeds to answer a series of routine questions: He holds a master's degree in education. He takes medication for high blood pressure. He has never been treated for mental illness or substance abuse. He understands that the charges against him carry a maximum penalty of 28 years in prison.

Then the judge comes to what she considers the most pressing point: Does Lynn truly understand the risk he faces by allowing the church to pay his legal fees? If Lynn's attorneys are paid by the archdiocese, their loyalty to their benefactor may put them at odds with his needs as a defendant in a criminal trial.

"You have been charged. You could go to jail," Hughes says gravely. "It may be in your best interest to provide testimony that is adverse to the archdiocese of Philadelphia, the organization that's paying your lawyers. You understand that's a conflict of interest?"

"Yes," Lynn replies.

The judge massages her temples and grimaces, as though she can't believe what she's hearing. For 30 minutes straight, she hammers home the point: Do you understand there may come a time that the questioning of archdiocese officials could put you in conflict with your own attorney? Do you understand that you may be approached by the DA offering you a plea deal, in exchange for testimony against the archdiocese? Do you realize that is a conflict of interest for your lawyers?

"Yes, Your Honor," Lynn continues to insist cheerfully, though his voice grows fainter as the minutes tick by. In one final plea for rationality, the judge asks if Lynn would like to consult with an independent attorney for a second opinion. He declines and returns to his seat, looking flushed and unhappy.

Lynn's lawyers, citing a gag order on the parties in the case, declined to allow him to comment for this article. The archdiocese also refused to comment, citing its emphasis on what it calls "moving forward." So far, Lynn's attorneys have simply argued that the case should be dismissed: Because charges of child endangerment are normally reserved for people directly responsible for kids – parents, teachers – Lynn's remove from the victims means his prolonged efforts to cover up the crimes were not technically illegal.

The court has rejected that argument, and the trial against Lynn and his co-defendants – all have pleaded not guilty – is scheduled to begin this winter. It may include videotaped testimony from Cardinal Bevilacqua, as well as the release of some 10,000 potentially incriminating documents. Lynn must know on some level that the church could be using him as a shield one last time in its systematic campaign to hide decades of monstrous abuses against children. But his willingness to sacrifice himself – his unswerving obedience to his superiors, even in the face of criminal charges – is what makes him such a loyal and devoted servant, all the way to the bitter end.

This is from the September 15, 2011 issue of Rolling Stone.

From The Archives Issue 1139: September 15, 2011