Editor’s note: This is part one of a two-part series. Tomorrow’s conclusion will explore what Pope Francis means when he calls Chile to become once again a “prophetic church.”

ROME – It’s a universally acknowledged reality of the sea that it’s never the tip of the iceberg that sinks a ship, but what lies under the water unseen. Yet, to the trained eye, the visible white mass usually is enough to warn of the dangers ahead and to change course.

In the case of Chile’s clerical sexual abuse scandals, Pope Francis first brushed against the tip of the iceberg in 2015, when he decided to transfer a Chilean bishop named Juan Barros, accused of having covered up abuse, to a southern diocese.

Yet Francis repeatedly ignored the alarms that came loud and clear. Victims of the pedophile priest Fernando Karadima, for whom Barros allegedly covered up, spoke with anyone who would listen, including members of the pope’s own Pontifical Commission for the Protection of Minors. The media, both in Chile and in Rome, kept the case in the spotlight. Chilean politicians sent a letter to the pope asking him to change course, and even some bishops spoke up against the nomination.

But Francis kept going, full steam ahead.

The inevitable collision came with a decision to send two papal envoys to Chile to investigate the Barros case. Their 2,300 page report, the product of 64 personal interviews, forced the pontiff to confront what was underneath the waters.

The document by Maltese Archbishop Charles Scicluna and Spanish Father Jordi Bertomeu remains confidential, but in the past two weeks, since the Chilean bishops have been to Rome and back, presenting their resignations to Francis, ample evidence has arisen showing just how big the iceberg is.

In the diocese of Rancagua, for instance, 14 priests who were part of a clan that called itself “La Familia” have been suspended pending investigation on allegations both of sexually abusing minors and of having consensual gay sex with adults.

Bishop Alejandro Goic, who until last week was the president of the Chilean Church’s National Commission for the Prevention of Abuses, has apologized for “my actions in this case,” and acknowledged that he hadn’t moved with appropriate nimbleness. He’s had to step down from the commission.

It’s also been made public that Father Óscar Muñoz Toledo, former chancellor of the archdiocese of Santiago, was removed from that position on Jan. 2, days before Francis’s visit to the country, after he actually reported himself for sexual abuse.

Though the details weren’t clear at the time, it’s now known that he sexually abused some of his nephews, who were minors at the time. This means the man tasked with taking the statements of some of Karadima’s victims was, at the same time, sexually abusing children himself.

In addition, former religious sister Consuelo Gómez left her congregation last year after being sexually abused on more than one occasion by a Chilean superior while the two were in Spain.

The Congregation of the Sisters of the Good Samaritan released a statement through the bishops’ conference acknowledging that they had known of the allegations, and that the way they had addressed the issue didn’t live up to “our mission and vocation.”

According to the former nun, the order told her to keep the abuses to herself and that they “had been her fault.”

Last Thursday, the Jesuits in Chile — Francis’s own order — announced through a statement that they had closed an investigation against Father Jaime Guzmán Astaburuaga on charges of sexual abuse of minors, and that the information compiled will be sent to the Vatican’s Congregation for the Doctrine of the Faith (CDF).

According to the terms of St. Pope John Paul II’s 2001 document Sacramentorum Sanctitatis Tutela, the trying of a case of a priest accused of sexually abusing a minor is exclusively reserved to the CDF, though the CDF can assign the case to a local church.

The allegations against Guzmán involve abuses that took place before 1994, meaning that under Chilean civil law, the crimes have passed the country’s statute of limitations, unless the Chilean congress passes a bill presented by President Sebastián Piñera in the past month aimed at lifting the statute of limitation for sexual abuse crimes.

Guzmán received a canonical sanction in 2012, and he’s been banned from public ministry and from being in contact with minors.

In an effort to comply with Francis’s request to move forward toward “transparency, truth, justice and reparation,” the statement by the Jesuits also disclosed that two other religious have been removed from public ministry in recent years for sexual abuse. They are Fathers Raúl González, denounced in 2011 by a former student for abuses which happened in 1999, and Juan Pablo Cárcamo, accused by a grown-up woman of abuse of conscience and sexual transgressions during a spiritual retreat.

In addition, revelations against the Marist brothers, who’ve already acknowledged decades-long situations of abuse of children, continue to arise.

Two of the closest collaborators of Cardinal Raúl Silva Henríquez, head of the Archdiocese of Santiago from 1961 to 1983, Fathers Cristian Precht and Miguel Ortega, have been found guilty of abuse.

Both Precht, a hero of the human rights movement until the allegations surfaced, and Ortega, who died in 2015, have faced new accusations in recent days, this time from victims of the Marist brothers, who say the two sexually abused children when visiting Marist facilities, including making sexual advances to teenagers who went for confession.

On May 21, at a closing Mass for a diocesan synod, Cardinal Ricardo Ezzati, accused by victims of covering up abuse and ignoring allegations, said the CDF had assigned him responsibility for six cases of clerical sexual abuse while he was in Santiago.

On Friday, his archdiocesan website published the names of the six priests and what their sentences had been. In the case of Precht, the site says he’d been sentenced to a five-year suspension of his priestly ministry, that he currently has no pastoral position, and that there’s a new investigation due to new allegations. Four others were suspended permanently and lost their clerical status, and another was suspended and died soon afterwards.

Two survivors, a doctor named Jaime Concha and a real estate agent named Jorge Franco, spoke to Scicluna and Bertomeu earlier this year about the abuses they suffered. They’ve also accused Father Alfredo Soiza-Piñeyro, who was defrocked in 2013 after allegations of sexual abuse reached the Congregation for the Doctrine of the Faith.

Soiza-Piñeyro gained national fame in 1987 when he mediated in the kidnapping of a colonel in the Chilean army, Carlos Carreño.

In a letter he gave to the bishops in Rome, Francis spoke of a Chilean Church guilty of destroying evidence, of hiding the importance of the allegations, and of having practicing homosexuals forming seminarians.

On the last point, there are reports dating back to 2011 of abuses in the seminary of San Rafael in Valparaiso. They include abuses of a sexual nature, but also of power and conscience: seminarians who were forced to swim naked with their superiors, and a man who today is the local bishop, Gonzalo Duarte García de Cortázara, publicly slapping an aspirant to the priesthood because he wouldn’t kiss him on the mouth. That incident is said to have happened in 1992.

Mauricio Pulgar, a former seminarian of Valparaiso, spoke with local news site The Clinic in 2011 and said that his superiors sent him to talk to a psychologist to overcome his “affectivity problems.”

“If you don’t like to be touched [on your private parts], you’re the one with a problem,” he said. “If you don’t like your lips to be grazed, you’re the problem. If you don’t like to walk around hugging, you’re the problem. Always, the deviant is you,” he said at the time, in allegations he’s repeated since.

Pulgar has spoken up against several priests in addition to Duarte, but nothing has come so far of the charges. Duarte is over 75, so he had presented his resignation to Francis even before the Chilean bishops traveled to Rome.

By now, it’s clear that the crisis of the Catholic Church in Chile is deep. Observers say that cleaning the house, undoing the damage, compensating survivors, and rebuilding trust in the institution and the faith among those in the pews will take decades.

Regardless of how many resignations from the bishops Francis eventually accepts, the challenges go well beyond the simple rolling of heads, as he’s said time and time again. There’s a “culture of abuse” and cover up that must “never again” be repeated, he wrote in a letter to Chilean Catholics on May 31.

RELATED: Pope to Chile: I’m ashamed we ‘didn’t listen’ on abuse

Traditionally, to choose a new bishop the Vatican relies on information provided by the local hierarchy and the papal representative in the country. In this case, however, the credibility of Archbishop Ivo Scapolo, the current papal ambassador in Chile, has been tarnished, with many at the grassroots asking for his resignation.

Francis still has a long road ahead after the Vatican’s ambivalent response to the various allegations, and his own, though his steadfast approach of the past 45 days, has garnered him the support of the New York Times editorial board, which back in January had gone after him for his defense of Barros.

However, in the meantime, at the grassroots level there are still men and women, “the holy people of God, faithful and suffering,” in Francis’s words, who are keeping the faith in Chile alive, answering his call to build a “prophetic Church.”

In the words of Chilean Father Mariano Puga, “I ask myself, what happens with the poor of the Church after the pope’s decision, after the allegations against the bishops? What happens with those who’ve baptized their children, who go to Mass on Sundays, who receive Communion? What happens with those who believe in Jesus and are outside of all these scandals?”

On June 1, Father Francisco Astaburuaga, one of a group of nine Chileans, some victims of sexual abuse, others of conscience, others who supported survivors, and seven of them priests, unknowingly answered that question after meeting the pope.

“I want to communicate to them [the laity], that always after the experience of the cross comes the resurrection,” he told journalists on Friday, the day of his arrival in Rome.

“What the pope is telling us with his actions and words is nothing else than an exhortation to being reborn, to the courage of making the conflict ours, looking at it in the face and confronting it with hope, that which comes from Christ. I’m convinced that we will all come out of this renewed in our faith, both the Church as a community as well as each faithful,” he said.

“The time has come for every Catholic in Chile to open generously to the dynamic of hope,” Astaburuaga said.