As stragglers hurriedly removed their coats and settled into the already packed pews in downtown Chicago on Sunday, the Rev. John Cusick walked to the middle of the sanctuary and offered a sort of apology for what he was about to say, explaining that “in the United States right now, you basically can’t say of much of anything without creating enemies.”

The din inside Old St. Patrick’s stopped and the congregation quieted.

“I’m very much in pain,” the priest said. Alluding to a series of executive orders from President Donald J. Trump that are designed to crackdown on undocumented immigrants and ban refugees from entering the country, he continued, “I had to say to myself, where is Christ in this?”

He said that over his 47 years as a priest it has sometimes occurred to him that just because something is legal does not mean it is moral. He offered up the death penalty and abortion as examples.

Then Father Cusick asked, “What we have seen since Friday afternoon, is it right?”

Sensing that some in the congregation might be uneasy about such a political hot topic being discussed in church, he said the issue went beyond politics.

“I don’t care about your politics. I’m apolitical,” he continued. “But I’m a follower of Christ and I preach Christ. My former pastor, may he rest in peace, said to me one day, ‘John, find where the poor, the broken and the discriminated are, and you will find where Christ is.’”

“Need I say anymore?” he asked.

He said the news over the past week pained him so much that he had “to do something this time,” which for him meant reaching out to an immigration activist and asking how he could help. He challenged those present to do something as well.

“And I ask all of you, whichever lever you pulled or line you filled in on Nov. 8, I don’t care. But I care when good people do nothing, and I do not want to be in that group,” he said.

“So I ask all of us, before your head hits the pillow tonight, answer one question: What will I do for the people living in fear who cannot come home right now to America where they live, who feel threatened?” he asked.

Applauding enthusiastically, the congregation rose to their feet to sing the opening hymn as Mass began.

The scene inside Old St. Pat’s was just one of many ways Catholics responded to President Trump’s first week. It began with some high-profile Catholics praising the president but ended with a slew of statements from bishops, Catholic universities and charities expressing shock at how quickly the administration moved in disrupting the lives of migrants and refugees.

On Jan. 23, the president signed an executive order reinstating the so-called Mexico City Policy, which prohibits U.S. tax dollars from paying for or promoting abortion overseas. Cardinal Timothy Dolan, archbishop of New York and head of the bishops’ pro-life committee, praised the executive order, calling it “welcome step toward restoring and enforcing important federal policies that respect the most fundamental human right—the right to life.”

A few days later, on Jan. 27, Vice President Mike Pence addressed the March for Life, a massive anti-abortion march held each January in Washington. His appearance, the first ever at the march for a vice president, drew praise from Boston’s Cardinal Sean O’Malley, an advisor to Pope Francis.

“I was very edified by the stance of the Vice President, which was obviously one of a person who is very deeply pro-life,” the cardinal wrote on his blog. “It was not an angry rant but a call for compassion and for understanding, a genuine call for the defense of all human life.”

Though the cardinals praised the Trump administration on abortion, they expressed some concern with his other actions affecting immigration, with hints of a refugee ban already circulating.

On Friday, news broke that the Mr. Trump had signed the executive order that bans Syrian refugees from entering the United States indefinitely, enacts a 120-day block on all refugees seeking entry into the country and reduces by half the total number of refugees the United States plans to resettle in 2017.

That development led the U.S. Conference of Catholic Bishops to publish its third statement of the week condemning a Trump executive order: The first condemned an executive order speeding up the proposal to build a wall along the U.S.-Mexico border; the second condemned Mr. Trump’s plan to pull federal funds from sanctuary cities; and the one released last Friday condemned the refugee ban.

“We believe that now more than ever, welcoming newcomers and refugees is an act of love and hope,” read the statement from Bishop Joe Vasquez, head of the bishops’ refugee committee.

That afternoon, the bishops’ migration and refugee office promoted an online campaign to get Catholics to contact their legislators about protecting the rights of migrants. By Monday, more than 16,000 had filled out an online form to contact members of Congress.

As demonstrators flocked to U.S. airports to protest the order, the bishops’ office of refugee and migration services coordinated with Catholic organizations to schedule volunteer lawyers headed to airports to offer assistance to families of those being affected by the order.

As the weekend progressed, several bishops added their voices to the mix.

On Sunday, Cardinal Blase Cupich of Chicago called the developments “a dark moment in U.S. history,” and Bishop Robert McElroy of San Diego said the president’s “executive order is the introduction into law of campaign sloganeering rooted in xenophobia and religious prejudice.”

That afternoon, about 500 Catholics gathered for Mass in front of the White House, praying for those affected by the president’s executive orders.

The archbishop of Washington, Cardinal Donald Wuerl, urged caution, writing on his blog that “the legal situation is still fluid and news reports are sometimes confusing” while acknowledging that “in the meantime, real people and real humanitarian concerns are being affected.”

The bishop of Portland, Maine, Robert Deeley, said in a statement that the order had “left many refugee families in Maine, as well as their family members still seeking entry into the United States, filled with anxiety and fear about what will happen to them.”

Many Catholic colleges and universities also weighed in, citing concerns about how the order would affect international students.

The president of the University of Notre Dame was among the first among high-profile Catholic colleges, saying in a statement on Sunday morning that the executive order harmed higher education in the United States.The Rev. John Jenkins called the order “sweeping, indiscriminate and abrupt.”

“If it stands,” he continued, “it will over time diminish the scope and strength of the educational and research efforts of American universities, which have been the source not only of intellectual discovery but of economic innovation for the United States and international understanding for our world.”

Leaders at Boston College also challenged the order, writing in a statement, that it was “contrary to American understandings of this nation’s role as a refuge and its place as a society that does not discriminate on the basis of religion or national origin.”

Calling the executive order “significant and concerning,” Georgetown’s President John DeGioia said in a statement that the Jesuit university “values the contributions of our international students, staff and faculty, and we are deeply committed to interreligious dialogue and providing a context in which members of all faith backgrounds are welcomed and encouraged to practice their faith.”

Across town, the Catholic University of America was measured in its response, urging calm and not criticizing the order itself.

“At this time we cannot know with certainty how recent executive orders will affect people seeking education, refuge and citizenship in our country,” President John Garvey said in a statement, urging international students to contact administration with any concerns.

By Monday afternoon, the heads of the bishops conference as well as the nation’s largest organization representing Catholic sisters had also weighed in.

The Leadership Conference of Women Religious accused the president of having “misplaced priorities” and said his executive orders “do nothing to make anyone more secure and may well have the opposite effect.”

“Women religious have been blessed to be able to accompany and serve immigrant and refugee communities across this country for a very long time,” the statement continued. “Halting or undermining the U.S. refugee resettlement program leaves vulnerable refugees, including women and children fleeing violence, in extreme danger and diminishes us all.”

The president and vice president of the U.S. bishops conference released a joint statement in which they defended the rights of Muslims and promised that the Catholic Church would “not waver in her defense of our sisters and brothers of all faiths who suffer at the hands of merciless persecutors.”

“Welcoming the stranger and those in flight is not one option among many in the Christian life. It is the very form of Christianity itself,” Cardinal Daniel DiNardo, president of the conference, and Archbishop José Gomez, the vice president, continued. “Our actions must remind people of Jesus.”

The mood among some Catholic leaders may shift yet again. The president is expected to announce his nominee to the Supreme Court Tuesday night. During the campaign, Mr. Trump promised to appoint someone who holds pro-life views.

Mr. Pence said last week that the nominee would be a person “who will uphold the God-given liberties enshrined in our Constitution in the tradition of the late and great Justice Antonin Scalia.”

If that promise comes to fruition, expect again a flurry of statements from some Catholic circles addressing the president—only this time with a return to a more favorable tone.

UPDATE, Feb. 1: Several other Catholic groups have also released statements opposing President Trump’s executive orders.  

Jesuit Refugee Service/USA said the order inappropriately targets refugees from Syria and other Middle East countries in a way that unfairly scapegoats these groups. The timing of the policies, released during Holocaust Remembrance week, reflects a lack of compassionate leadership, the organization said in a Jan. 27 statement.

“These provisions fly in the face of the core American values of welcoming persecuted families and individuals who come to America to rebuild their lives in safety and dignity and to contribute to the richness of our communities,” the statement said.

The Catholic Theological Society of America board members called President Trump’s executive orders on refugees “[M]orally unjust and religiously dangerous.” In a Jan. 31 statement, they wrote that the president’s actions “violates both the norms of Christian ethics and the human rights that all can affirm no matter what their faith.”

“Our duties to refugees and other severely vulnerable migrants is also based on the conviction that every man, woman, and child is created in the image and likeness of God and has a dignity that must be respected by all,” the board wrote. The statement highlighted the importance of regulated borders, but noted that “national borders, however, never set absolute limits to our moral duties to other human beings, especially when they are in great danger.” Wyatt Massey