The young man studying at Mundelein Seminary to become a Catholic priest seemed anguished as he vented to Cardinal Blase Cupich about the clergy sex-abuse scandal that threatens to topple Pope Francis and drive more people away from the faith.

“I’m hurting, I can’t sleep, I’m sick,” the seminarian told Cupich during an Aug. 29 gathering at which the cardinal spoke to about 200 future priests enrolled at the seminary, according to another person who was there and spoke with the Chicago Sun-Times but asked not to be identified.

The seminarian told Cupich he was a young boy during the last scandal, in the early 2000s — amid a renewed wave of child-rape allegations against priests and cover-ups by their bishop bosses — and “thought this was over,” that the bishops had done their jobs.

Cupich thanked the man for speaking up and said he, too, was sick over the situation.

Minutes later, though, the cardinal said something that struck some of the seminarians as “tone-deaf.”

“I feel very much at peace at this moment. I am sleeping OK,” Cupich said, according to the person in attendance, a man studying to be a priest, who recalled that some fellow seminarians shook their heads in “disbelief.”

The source said Cupich also told the group that, while the church’s “agenda” certainly involves protecting kids from harm, “we have a bigger agenda than to be distracted by all of this,” including helping the homeless and sick.

That account was confirmed by other sources, including another seminarian also present at the gathering.

One of them said he decided to speak with the Sun-Times because so many Catholics “are hurting,” the cardinal’s remarks were so “non-pastoral,” and “the people of God need to know that their seminarians care” and “aren’t going to repeat the mistakes of the past — not only not repeat them but have them cleaned up.”

Cupich, who was at the north suburban seminary for a spiritual retreat and meetings, speaks there every year. His talk centered on the current scandal. He spoke of seminaries being under a greater “spotlight” because of sexual misconduct — with the future priests knowing they will need to deal with a distrustful flock and help clean up the wreckage of a battered church.

The Mundelein seminarians come from across the United States and also from outside the country.

The tone of some of their questions, according to people who were there, indicated the sex-abuse crisis is very much on their minds — and that, even as Cupich urged them to trust him and Pope Francis, some seemed reluctant to put blind trust in bishops to fix things.

Neither Cupich nor Chicago archdiocese spokeswoman Paula Waters responded to interview requests.

Mundelein’s rector, the Rev. John Kartje, said, “The cardinal would have to speak for himself, just like the students are speaking for themselves.”

According to the sources who spoke with the Sun-Times:

• Cupich began his 15-minute talk, held in the dining hall and closed to the public, by describing “expectations” for seminarians, alluding to two hot-button topics relating to priestly training grounds — disgraced ex-Cardinal Theodore McCarrick, who allegedly sexually preyed on male seminarians out East for years, and “inappropriate” behavior among male seminarians.

Those studying to be priests, as well as those already ordained, are supposed to abstain from sexual activity, with gay sex regarded as a sin.

A “moral uprightness and virtuous life” is important, Cupich told the seminarians. “We don’t tolerate inappropriate behavior,” he said, encouraging seminarians to come forth if anyone solicits them for sex or makes suggestive comments.

Cupich said that shortly after being appointed Chicago’s archbishop in 2014 by Pope Francis, a “number” of Mundelein students were “dismissed” for inappropriate conduct, which he didn’t elaborate on.

Cupich’s comments were notable to some in the audience for appearing to focus more on wrongdoing by seminarians and less on them being victimized, as allegedly occurred with McCarrick, who resigned from the College of Cardinals in July and was ordered by the pope to a “life of prayer and penance” over accusations that he sexually abused minors and adult seminarians over a span of decades.

• Cupich seemed taken aback when seminarians mentioned during a 45-minute question-and-answer session that some former students who left Mundelein after getting into trouble there are now enrolled at another Catholic seminary in an out-of-state diocese.

Cupich told the audience that, to his knowledge, there’d been no inquiries from other seminaries about the men, as would be required. Cupich appeared concerned and said the matter would be looked into promptly, according to those present.

A spokesman for the out-of-state diocese confirmed that two seminarians previously had been in a priest “discernment” program in Chicago. But the circumstances of why they left Mundelein had been “thoroughly” investigated, and there was “no evidence” found “precluding them” from joining the new diocese, according to the spokesman, who said part of the “due diligence” included talking with “various” church leaders in Chicago.

The Sun-Times is not identifying the men nor the diocese because of the many unanswered questions about the matter.

• Cupich told the Mundelein seminarians in response to a question that he doesn’t buy the argument advanced by some in the church that homosexuality is at the root of much of the sexual abuse by priests. He said the “facts don’t bear that out, and it’s wrong” to blame a group of people that way.

Cupich also said he had never heard of abusive priests “passing kids around as though there was a ring” or “working together in a coordinated way” until recent revelations emerged about rampant clergy sex abuse in Pennsylvania in another recent church scandal.

Cupich indicated he believes the overall crisis has been fueled in part by a culture in which priests feel “privileged and protected,” what he termed “clericalism.” He said that continues and can carry a “homosexual tinge,” which he didn’t explain.

He also said a gay “subculture” can sprout in the church and that “that’s inappropriate” because it amounts to a “clique.”

Whether clerics are “gay or straight,” the witnesses said Cupich told the seminarians, they should be living “a chaste life” and “keep their commitments.”

Cupich, who once was the rector of a seminary in Columbus, Ohio, told the Mundelein group his comments and his record show he views this subject seriously — which appeared to be a response to criticism last month by a former Vatican official, Archbishop Carlo Maria Vigano, who said in a public letter that Cupich advances a “pro-gay ideology.”

• Cupich said seminarians should trust in Pope Francis even though the pope has been silent on whether Vigano was correct in saying Francis had allowed McCarrick to stay in ministry despite knowing he’d been preying on seminarians.

Vigano’s claims have led to calls for a larger investigation and, from some quarters, to calls for the pope’s resignation.

The pope is “calling us . . . to have patience” and let the truth emerge in an “organic way,” Cupich said, adding the pope isn’t “running away from a conflict” but is just being “very strategic,” according to seminarians.

Cupich said he agrees with the pope that the news media should be the ones to investigate Vigano’s allegations, which also included claims that McCarrick went to bat with the pope to get Cupich appointed Chicago’s archbishop in 2014. Cupich has said he doesn’t know whether that’s true.

• One seminarian told Cupich he seemed to be telling them they need to keep their heads down, with the cardinal telling the students not to be “distracted from what you have to be doing in your formation” and let those dealing with the crisis “do their jobs.”

• Though the Archdiocese of Chicago — which includes Cook and Lake counties — has paid out roughly $200 million in legal settlements over the years for sex-abuse claims, Cupich also told seminarians that “our record’s clean,” and “we are not what happened” in Pennsylvania.

• While supporting the pope for staying silent on Vigano’s claim, Cupich lambasted Vigano for not offering proof of his allegations. Cupich said he’d support Vigano appearing before a church “tribunal” to test his assertions under oath.

“I think that he needs to take responsibility for what he says” and “back up what he says,” Cupich said.

Noting that Vigano has been quiet since releasing his bombshell allegations on Aug. 25, Cupich said, “Why is he hiding? Why is he hiding?”

One seminarian who spoke up at Mundelein told Cupich this isn’t a time for “attacking” Vigano or the pope, the sources said. “There needs to be an investigation” into Vigano’s claims, the seminarian told the cardinal.

Cupich said of Vigano — who is part of the more conservative or traditional wing of the church, while Cupich and Pope Francis are seen as more liberal or progressive and have softened the church’s tone toward homosexuals — that he didn’t mean “to attack him personally” but wanted to point out the “conflicts” and “inconsistency” in what he’s said.

Cupich also said, “If I say what he says is credible, then I have to say what he’s saying is credible about me.”

In his letter, Vigano said of Cupich: “Regarding Cupich, one cannot fail to note his ostentatious arrogance, and the insolence with which he denies the evidence that is now obvious to all: that 80% of the abuses found were committed against young adults by homosexuals who were in a relationship of authority over their victims.”

• Cupich also tried to rally the seminarians, saying the church needs their “idealism” and that perhaps they’re being chosen by God to help fix things.

One of the seminarians who spoke with the Sun-Times said the abuse crisis makes him want to be a priest even more because people are suffering so much.

“I am convinced that this moment is going to mature you and the church,” Cupich said to the crowd, recounting a biblical saying about gold being “tested by fire.”

Cupich also warned of “demonic forces” and told the seminarians that all of them will be tested at some point.

Predator priests “were loners,” so build “good, healthy human relationships,” Cupich told them.

Cupich also recounted speaking to a group of Chicago police officials and observing that the police department exhibits “a version” of clericalism in which officers “cover” for each other when they do wrong.

He said he told them: “That is the road to perdition for any organization.”

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