WEYMOUTH, Mass. — A shy smile creased the face of Father Charles Murphy as the congregation’s applause enveloped him.

Father Murphy had just returned to public ministry after what he called “dark days.” He had fought a 30-year-old sexual abuse claim that a civil court eventually dismissed and a Church review board declared unsubstantiated.

His ordeal began with what another Boston priest called the Church’s “KGB cure” in response to the abuse crisis. A priest facing an abuse claim must cease his ministry, vacate the rectory as if he were guilty, and then prove his innocence.

It was Divine Mercy Sunday, nearly two years since the 72-year-old priest had last celebrated Sunday Mass at St. Francis Xavier Church. He walked in past a “Welcome Home” sign.

With three priests by his side, he paused behind the altar until the second round of clapping slowed.

He looked at the people who had held weekly prayer vigils for him, helped with his legal bills and given him calls and letters of encouragement.

“You have been my consolers, my faithful companions. My heart is filled with so many emotions,” he said.

Father Murphy’s voice was steady. “I am filled with gratitude to you. Your friendship, the Masses you had offered for me — these all helped me to live with the pain and suffering of not being able to exercise my priestly ministry.

“You eased my loneliness. Your hopes urged me to increase my trust in the Lord. You inspired me to read sacred Scripture so we were united in the word of God.

“My hope has become more personal and alive. Now, my faith knows no bounds. I have experienced a new presence of Christ in my life. May we always be aware that wherever we are, Christ is with us,” Father Murphy concluded as more applause erupted.

When he distributed Communion, some parishioners patted his arm. Parents held up babies for him to bless. After Mass ended with a fourth wave of applause, Father Murphy greeted hundreds of well-wishers.

“He’s a very holy man,” said parishioner Kathy Hubbard, a mother of 11. “He was devastated.”

Janet Peruzzi said, “He’s a priest who loves his priesthood and wouldn’t do anything to jeopardize it.”

“No one believed it,” parishioner Katherine Morrissey said. “He’s beloved here. This took years off his life.”

Dark Days

“Father Murphy is coming down from a long period of turmoil,” said his attorney Timothy O’Neill. “Unfortunately, the institution’s been fighting to protect itself, not the individual priest.

“But to be fair, the Church has been totally overwhelmed by the number and extent of abuse claims,” O’Neill said. “I’m not denying the holocaust, but you can feel pretty helpless when you’re removed from ministry and you know you didn’t do anything. These guys are pretty much on their own.”

The accusations made national news when the story broke. He and 14 others were named in a civil suit that claimed alleged abuse of students at the Boston School for the Deaf between 1944 and 1977. Father Murphy, who is hearing-impaired, served as director of counseling there in the 1970s.

All the claims were later withdrawn or dismissed by the court. But the story of Father Murphy’s exoneration by the Church made only local news. It rated a brief release in The Pilot, Boston’s archdiocesan paper.

According to the archdiocese’s Office of Child Advocacy, 71 complaints were filed against Boston-area priests from July 2003 to December 2005. In 32 of those cases, the review board did not find that probable cause of sexual abuse of a minor had occurred.

The Norms of the U.S. Conference of Catholic Bishops state: “When an accusation has been shown to be unfounded, every step possible will be taken to restore the good name of the person falsely accused.”

Boston archdiocesan spokesman Terrence Donilon and review board members declined to explain what steps are taken to restore a priest’s reputation.

“We call it the Humpty-Dumpty restoration process,” said one Boston priest. Another said, “That policy is just lip service.”

The defendants’ attorneys in the Boston School for the Deaf cases had portrayed the plaintiffs as “opportunists trying to cash in on publicity surrounding the $85 million paid in 2003 by the archdiocese to victims of clergy sexual abuse,” according to The Patriot Ledger, a suburban Boston paper.

At the time of that record settlement, Forbes magazine noted, “Litigators have parlayed the priest crisis into a billion-dollar money machine. Lawyers are lobbying states to lift the statute of limitations on sex abuse cases, letting them dredge up complaints that date back decades.”

“Father Murphy’s case was totally without substance,” said O’Neill. He was first charged just with walking into a room where a girl was changing. When it was obvious that charge would get dismissed, O’Neill said, the same woman then later filed another claim charging the priest had fondled her.

Joseph Doherty Jr., who represented four other defendants, said in a Boston Globe report, ‘‘There was no credible evidence to substantiate any of these claims.”

O’Neill said that one difference between this case and some earlier ones was that these defendants would not settle in mediation but waged a vigorous two-year civil defense. “Most priests just don’t have the money for those legal fees,” he said.

“Some people were just in it for the money,” said Father Edward Sherry, pastor of Church of the Nativity in Merrimac, Mass. The archdiocese had paid off a 30-year-old abuse claim against him in 2003, but then found on review that the charge lacked validity. He returned to ministry in 2005.

“I’m not bitter. I knew I was innocent,” Father Sherry said in an interview. “The archdiocese is questioning claims more now than it did before.”

Father Robert Carr of St. Benedict Parish in the Boston suburb of Somerville echoed that theory. “When the Church would not settle right away, cases started to drop off,” he said.

The legal path was steep, costly and painful, Father Murphy noted in his returning homily. But as he told parishioners, “We’ve been tried by fire and have not been found wanting. We have journeyed from ashes to Easter.”

Now their “long Lent” is over. Now there is joy: hugs and tears and smiles all around. He is home.

There is one Detroit-based lay advocacy group for priests, Opus Bono Sacerdotii (Work for the Good of the Priesthood), which gives referrals and moral and spiritual support.

And the Confraternity of Catholic Clergy, based in Marysville, Pa., helps diocesan priests with fellowship and formation. Father John Trigilio, its president, warned against a “miscarriage of justice” by “over-reacting to the clergy sex scandals by denying priests their natural right to due process, legal defense and the presumption of innocence.”

He said in an interview, “We can do and must do both: protect the innocent and punish the guilty. The media have a feeding frenzy whenever someone is arrested and often that same media is low key if not silent when the same person is exonerated.”

Gail Besse is based in