WORCESTER — When students return to the Nativity School of Worcester in the fall, they will be greeted by a familiar sight: Pride and Black Lives Matter flags fluttering in the breeze above the school, tucked just off Interstate 290 near downtown.
The flags represent a steadfast rejoinder to those who believe such symbols have no place at a Catholic school.
In June, Bishop Robert J. McManus, of the Diocese of Worcester, stripped the all-boys middle school of its right to call itself Catholic over its refusal to take down the flags, which McManus said promote political messages contrary to Catholic teaching. Additionally, the school has been barred from celebrating Mass and the sacraments.
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But months later, school leaders say the diocesan rebuke has done little to dim Nativity’s commitment to what they see as symbols of inclusion. The display of the flags, they say, is actually driven by Catholic values, including Catholic social teaching and the Jesuit ideal of cura personalis, care for the whole person.
“Why we exist is trying to give students who come from underresourced communities the opportunity to reach their full potential,” Nativity’s president, Thomas McKenney, said in his office at the school. “I think part of that, too, is respecting human dignity.”

The controversy sparked a surge in fund-raising for the school, which said it received more than $100,000 from more than 1,000 donors in the week after the decree was announced. Although the school can no longer have monthly Mass on its grounds, students and teachers will attend at a church that welcomes them, McKenney said.
The dispute highlights a deepening division within the American church in recent years, between those who emphasize Catholic teaching on social issues like abortion, and those who focus on teachings about social justice.
“What truly is a Catholic school? Is it a Catholic school if there’s a cross on the wall and we say prayers and we go to Mass?” said John Reyes, the research director of the Roche Center for Catholic Education at Boston College. “Or is it a Catholic school because we have definitive positions on certain contemporary culture war issues?”
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In defending his decision, McManus said this week that he was following new guidelines on the identity of Catholic educational institutions recently set out by the Vatican. McManus expressed disappointment that his suggestion that the school fly alternative flags that read “End Racism” or “We are all God’s children” was “apparently not considered.”
The Catholic faith calls people to love each other and themselves with no regard for race or gender, McManus said in a statement.

“That truth of the Catholic faith cannot be supplanted by any other social agenda,” he said. “Any division that exists [in the church] today is, in my mind, due to a lack of understanding by many Catholics of these basic principles of our faith.”
The juxtaposition of modern liberal attitudes about inclusion and diversity with Jesuit teaching that has roots in the 16th century permeates the Nativity School from the morning assembly to the last bell.
The students are taught the works of both Ibram X. Kendi, the contemporary scholar and antiracism activist, and St. Ignatius of Loyola, the Jesuits’ founder. Crucifixes share wall space with a bulletin board highlighting prominent LGBTQ+ people.
On a recent sunny morning, while many of the city’s other middle-schoolers slept in, Nativity students lined up at the front doors for a daily ritual — shaking hands with the school’s principal and president.
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During the school year, Nativity students are in class from 8:30 a.m. to 5:30 p.m., and for much of July, they were back at their desks and out doing service projects for summer session.

After breakfast and silent reading, morning assembly began with attendance and announcements. Then one of the teachers played a YouTube video of “The Daily Show” host Trevor Noah interviewing Kendi and author Jason Reynolds about their young adult book on racism in America. After it ended, students’ hands shot in the air to answer questions about the video.
Then, the whole room grew solemn as another teacher read a prayer and some of the students requested prayers for loved ones. The students then filed out to class through a door with a crucifix over it.
The first Nativity middle school was founded on the Lower East Side of Manhattan in 1971 by Jesuit priests who felt the predominantly Hispanic community was not well served either by the public schools or the Catholic schools, according to Daniel Pérez, executive director of the NativityMiguel Coalition, which supports Nativity model schools nationwide.
“So the idea was, could we get these young boys from the neighborhood for . . . three years of their academic careers, hone them, let them learn about their talents and what their interests are, and then could we prep them for the best high schools in the city?” Pérez said.
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Nativity Worcester was founded along those lines in 2003 by senior administrators at the College of the Holy Cross. Since its inception, in a church basement, the middle school has been free of charge, which requires a large fund-raising operation to sustain.

Today, the school has an enrollment of 59 students across four grades. Most classes are staffed by two, if not three, instructors. The school spends about $25,000 per pupil annually, in line with some of the state’s richest suburban public school districts, McKenney said.
Admission is limited to Worcester families with incomes of less than about $50,000 a year. The school received approximately 40 applications for 15 slots in the fifth-grade class that started this summer, McKenney said.
During the school year, students are required to participate in after-school clubs and sports. The school also provides a weekly food pantry to families, brings in a community bank every month that provides high-interest savings accounts for parents, and has even connected families facing homelessness to housing.
“It feels less like just a middle school and more just like a hub where we can connect the students and their caregivers to all the different things that Worcester has to offer,” principal Andrea Munar said.
The school also commits to supporting students through their college graduation and employs two staff members to do it.
Jacob Vázquez, a 2011 Nativity graduate who heads the scholarships division of the Greater Worcester Community Foundation, credits Nativity’s constant support with much of his success.
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Sitting in the school’s lobby after giving a presentation to students about his work, Vázquez recalled that Nativity teachers spent hours helping him with his college essay when he was in high school.
“There was not one time that I felt afraid to ask Nativity for help,” Vázquez said.
McKenney says Nativity’s model is working. All alumni who were supposed to graduate from high school last spring received their diplomas, and 90 percent of the school’s alumni who recently graduated from high school are headed to four-year colleges in the fall.
The strong demand for slots at Nativity (it also plans to open a girls’ division in the coming years) stands in stark contrast to Catholic education broadly, which has seen plummeting enrollment in the state and nationally in the past 30 years.

Conservative US Catholics, meanwhile, see themselves as holding the line against encroaching secularism and the dilution of Catholic identity into something more palatable to progressives yet less true to the faith.
In a May op-ed in The Telegram & Gazette about flags at the Nativity School, McManus was blunt.
“So to the Board of Nativity School,” the bishop wrote. “The question is simply this: Which identity do you choose?”
At Nativity, which could appeal the bishop’s edict to the Vatican, they see that as a false choice.
Asked about Nativity’s Catholic identity, the first thing that came to eighth-grader Jensy Ramos’s mind was not prayers, Mass, or religion class.
“Everyone is welcome,” he said. “Because that is what God would want.”
Alexander Thompson can be reached at alexander.thompson@globe.com. Follow him on Twitter @AlMThompson