Mahony later approved a secret $1.3 million payment to two men who said they had been abused by the priest, Father Michael Stephen Baker, from 1984 to 1999. The cardinal arranged for the priest to quietly retire from the Catholic Archdiocese of Los Angeles in late 2000.
"No one at the Archdiocese of Los Angeles, including Cardinal Mahony ... reported Baker's sexual abuse of children to the authorities, to the parents of the abused children or to any other foreseeable victims. Nor did they attempt to find out all the children that he had molested."
Baker, now 54, allegedly molested at least nine youths beginning in 1976, according to interviews with victims, relatives and lawyers.
It was not until recent weeks that Mahony, under increasing pressure to reveal the names of clerics accused of sexual misconduct, reported Baker to law enforcement.
On Tuesday, Mahony faxed a two-page letter to about 1,200 priests in the archdiocese, acknowledging that he had mishandled the case.
"As your archbishop, I assume full responsibility for allowing Baker to remain in any type of ministry during the 1990s," Mahony wrote. "I offer my sincere, personal apologies for my failure to take firm and decisive action much earlier."
The letter, addressed to "My Brother Priests," warned of an upcoming media story on Baker. The Times has been preparing an article about the priest. "You need to be aware that such a story could come anytime now, and you need to be aware of the seriousness of this case," Mahony wrote.
The cardinal also notified the priests that archdiocese leaders have now learned of more allegations of sexual misconduct against Baker. He is one of at least 30 current and former priests from the archdiocese under investigation by criminal authorities.
In a series of interviews with the Times, Baker described going to the offices of the archdiocese in 1986 and telling Mahony of his problem with sexual abuse. He said that in one meeting, an archdiocese lawyer suggested calling the police but that Mahony said no.
The cardinal said in an interview that he could not recall the discussion with Baker.
The case is emerging as a pivotal one for Mahony and archdiocese leaders as they continue to grapple with the sexual abuse scandal that has hit the Roman Catholic Church. In an interview last month, Mahony called the Baker case the one "that troubles me the most."
The cardinal has sought to portray himself as a defender of young victims and an advocate of cooperating with criminal investigations. At Pope John Paul II's historic meeting with American cardinals in Rome last month, Mahony backed a "zero tolerance" policy for sexually abusive priests.
But leaked e-mail correspondence between top archdiocese officials reveals that Mahony was reluctant to turn over Baker's name to police as recently as late March.
The cardinal answered some questions about Baker last month but declined in the past week to be interviewed. An archdiocese spokesman cited Mahony's workload and recovery from a recent blood clot in his lung.
In an interview last month, the cardinal said the archdiocese had few options in dealing with Baker because the allegations against him were unproven. "Our biggest problem was that ... he wasn't found guilty of a criminal act," Mahony said. "That's a big problem."
In his letter to priests, Mahony did not disclose his failure to notify police when he learned about Baker's alleged abuses against minors in 1986 and again in 2000. But he wrote, "If I had known in those years what I discovered in early 2000, I would have dismissed him from all ministry and requested his dismissal from the priesthood in the late 1980s."
Of all the cases involving archdiocese priests facing claims of sexual abuse, Mahony said, Baker's is most troubling because he allegedly molested a number of children in the 1970s, '80s and '90s and continues to live in the area unsupervised.
Born and raised near Pasadena, Baker attended St. John's Seminary in Camarillo. Ordained in 1974, he initially served as an associate pastor at St. Joan of Arc parish in West Los Angeles for two years before transferring to St. Paul of the Cross in La Mirada.
Gregarious and charismatic, Baker was so well-liked at St. Paul that several families followed him in 1982 when he was transferred to St. Hilary in Pico Rivera. Baker was brought in as administrator and associate pastor at a time when parishioners were deeply divided along ethnic lines over a nun's alleged physical assault of a young Latino pupil at St. Hilary Elementary School.
Baker was instrumental in pulling the parish together, church officials said. He helped introduce a Sunday morning mariachi Mass and organize an annual Mexican fiesta that appealed to Latino families.
"He speaks Spanish fluently," said Deacon Arturo Barragan, who served with Baker at St. Hilary. "He has a capability of understanding the experience of the Mexican people. He has been very in touch with their culture."
Baker also was known for his active involvement in youth groups and teen clubs. He frequently took altar boys to the movies and on overnight trips.
The first incident of alleged abuse that has come to light took place in 1976 when Baker invited a 9-year-old altar boy to spend the night at St. Paul's rectory after a church-sponsored New Year's Eve party.
"That night was the beginning of a near-decade-long nightmare," the alleged victim, now 34 and living in West Hollywood, wrote recently in a memo to his attorney. "I knew what was happening was wrong, but felt trapped and would often just stare at the digital clock on the nightstand, afraid to go to sleep ... "
The Times does not identify victims of sexual abuse without their consent.
The man recalled in an interview with the Times that Baker took him on trips to Palm Springs, Newport Beach, Reno and Chicago. He said the abuse escalated to oral sex and that Baker occasionally whispered to him, "You're the son of God."
Years later, Baker expressed remorse in a letter to the man. "I know very well the confusion and hurt of the past and especially my responsibility in that," Baker wrote on Jan. 29, 1994. "I don't know what I can ever do."
Eight other people have alleged that they were molested by Baker in the late 1970s and '80s, according to interviews with them and their lawyers. Two brothers say Baker began abusing them at St. Hilary in 1984 when they were 5 and 7 years old.
In September 1985, Mahony was appointed head of the Los Angeles Archdiocese. The following summer, at an annual series of retreats for archdiocese priests, Mahony invited anyone who had engaged in sexual abuse to talk to him privately.
"We said to priests, 'If you have a problem or had a problem, it's really beneficial to step forward now,'" Mahony recalled in last month's interview. "We made it clear that, if you told us, we would follow the policies."
The procedures included removing a priest from ministry and referring him for evaluation while the archdiocese investigated any allegations, Mahony said.
In a series of interviews with the Times, Baker declined to comment on specific allegations of abuse. The priest said he admitted in a private meeting with Mahony in December 1986 that he had engaged in sexual abuse of minors.
"I told Mahony I had a problem," Baker said in one of a series of interviews with the Times. Mahony did not ask for specifics and appeared willing to let him remain in the priesthood, Baker said. "He was very solicitous and understanding. I was glad I brought it up."
That evening, Baker said, he received a call from Msgr. Thomas Curry, the vicar for clergy who oversaw all priests. Curry directed Baker to return to archdiocese headquarters the next day.
When he arrived, Baker said, Curry was joined by Mahony and John P. McNicholas, the archdiocese attorney. At the meeting, which lasted about 30 minutes, Baker said he was asked the extent of his problem. Baker said he disclosed that "two or three" victims were involved and vowed not to engage in any future sexual misconduct.
"I don't recall them pressing me for details, and I didn't give them any," he said.
At one point, Baker said, he became startled when McNicholas blurted, "Should we call the police now?" Baker said he recalled Mahony's response: "No, no, no ... "
The cardinal has provided conflicting accounts of his discussions with Baker.
Initially, he said last month that he had no recollection of the priest speaking to him about abusing boys. Mahony acknowledged that he would probably remember such a meeting if it had occurred.
Later, the cardinal said he thought Baker had approached Curry. Curry, now bishop of Santa Barbara, said he could not recall the Baker meeting either. "I just don't remember," he said.
On Tuesday, Mahony confirmed in his letter to archdiocese priests that Baker had confessed to him.
"Sometime in late 1986, Baker disclosed to me that he had problems in the past of acting out sexually with two minors," Mahony wrote.
Priests and parents at the three parishes where Baker had served until 1986 said the archdiocese failed to inform them about any reported sexual abuse by Baker.
In explaining his response, Mahony told the priests: "Baker was sent to a treatment center for evaluation and recommendation for his future. Following treatment, it was decided that he could do specialized priestly ministry not related to children and youth. He was subsequently given various ministries, such as special outreach to our retired priests."
Mahony also required Baker to undergo continued counseling and banned him from having one-on-one contact with minors.
The cardinal blamed Baker for not being honest during his twice-a-month counseling sessions.
"Baker's truthfulness was questionable," Mahony said in an interview, adding that "we never found any evidence of cooperation. He deceived his therapists, everybody."
In addition, Baker continued to have frequent access to children over the next 14 years while he was assigned to nine different parishes. Six of the churches where Baker worked had elementary schools adjacent to the rectory: St. Thomas the Apostle in Los Angeles, St. Elizabeth in Van Nuys, St. Linus in Norwalk, St. Mary in Palmdale, St. Lucy in Long Beach and St. Columbkille in South-Central Los Angeles.
Records and interviews also show that Baker was sent to at least three parishes to fill in for pastors who had either retired or been transferred, leaving no superior to monitor his day-to-day activities.
"Mainly, I was a pinch-hitter to keep things running smoothly," Baker said of his relief duties.
In his message to priests, Mahony said the archdiocese received no reports of sexual abuse involving Baker until two years ago.
"Early in ... 2000 we learned that two men in Arizona were preparing to sue Baker for past sexual abuse," Mahony wrote. "Once we became aware of that situation, he was removed immediately from all priestly ministry in accordance with the policy in effect at that time."
Mahony did not include in his letter that the archdiocese had received a 14-page letter of complaint that said Baker had continued to molest the two men for 13 years after the priest confessed to the cardinal in 1986. Nor did Mahony mention in the letter that he authorized a $1.3 million settlement with the two men and that the archdiocese insisted the deal remain secret.
The Times obtained a copy of the letter of complaint that was sent to the archdiocese in May 2000 by Tucson attorney Cadigan on behalf of the two men, who are brothers now living in Mexico. The letter of complaint describes the alleged abuses in detail.
At about the same time Mahony returned Baker to ministry in 1987, the two brothers and their mother moved to Guadalajara. According to the letter of complaint, Baker made the first of many trips to Guadalajara to visit the boys in the spring of 1988.
"Baker also flew [the brothers] from Mexico to Los Angeles, Palm Springs and Arizona approximately 15 times and, during the visits to Los Angeles, had the boys sleep with him [in] the rectory, where he molested them," the letter of complaint alleges.
The document also states that Baker provided the brothers with alcohol when they were young minors. The alleged abuses continued until 1999, according to the letter of complaint. The two men said they remained silent because Baker had threatened them if they told anyone and they did not want to hurt their mother, who had befriended the priest and regularly received money from him.
After receiving the letter of complaint, attorneys for the archdiocese and Baker quickly offered to settle, Cadigan said. They agreed to pay the brothers $1.3 million, among the largest settlements at the time for victims of sexual abuse in the archdiocese.
"I have never had a case in my 19 years of handling sex abuse claims that settled this quickly for this kind of money" without even filing a lawsuit, Cadigan said. She concluded that archdiocese officials knew "the allegations against Baker were true, there would be more victims, and they didn't want any publicity. What they were buying was silence."
Baker said he agreed to pay about half of the settlement from his own funds.
"I didn't want to fight it," he said. "I didn't want to go public and didn't want anyone to go through any more pain."
At the end of 2000, Mahony's aides arranged for Baker to resign from the priesthood. The archdiocese provided Baker about $10,000 in severance pay and 18 months of health insurance coverage.
The pastor at St. Camillus de Lellis near USC, where Baker last served, said he was told by a top aide to Mahony that the proper authorities had been notified about Baker in late 2000. Father Chris Ponnet said he had assumed the out-of-court settlement reached with Baker's victims included a jail term or probation.
"When something like this happens and a child ... is victimized, I've always believed it was ... a crime," Ponnet said. "I was always under the impression that if a crime had occurred, with or without the settlement, the appropriate police and others would be working with us."
But it wasn't until early this year, as the sex abuse scandal mushroomed and Mahony came under pressure to reveal the names of eight priests who had been previously accused of sexual misconduct, that the cardinal turned Baker's name over to police.
Even then, the cardinal was hesitant to cooperate, documents show.
According to confidential e-mail leaked to radio station KFI in April, Baker was among the final three names Mahony had not provided to law enforcement. In a March 27 e-mail to his top advisors titled "Our Big Mistake," Mahony scolded the archdiocese lawyer, Sister Judy Murphy, for resisting his suggestion that she "consult" with the Los Angeles Police Department about the three names.
"If we don't, today, 'consult' with the [LAPD] about those three names, I can guarantee you that I will get hauled into a Grand Jury proceeding and I will be forced to give all the names, etc.," Mahony wrote.
"There is no middle ground on this; we are losing the battle because we are somehow 'hiding' those three."
On March 30, Murphy reminded members of the cardinal's inner circle that Mahony was the one who resisted giving up Baker to police until the day before his "Big Mistake" memo.
"If you all remember, permission to do this was not given until Tuesday," Murphy wrote. "He was reluctant about [Baker]."
After the Times reported on April 17 that Baker was being investigated by police, Mahony authorized pastors at a dozen parishes where Baker had served to make an announcement during weekend Masses in late April. The statement, which came 15 years after Mahony first learned of Baker's past, encouraged anyone who had information that might assist investigators to contact the LAPD.
"Our faith teaches us that children are precious in God's eyes," the statement concluded. "Let's work together to make our homes, parishes and schools safe havens for all our children."
Times staff writers Ralph Frammolino, Beth Shuster and Richard Winton contributed to this report.