Arch Street United Methodist Church began providing Flores with sanctuary in November. On Wednesday, he left the church after being granted a waiver that would defer his deportation while his immigration case moves forward, his lawyer said. The waiver made him eligible for a special visa granted to victims of crimes who have cooperated with police.

The day was a win not only for Flores but for the larger sanctuary movement, which has openly challenged the Trump administration crackdown on illegal immigrants.

As Flores walked out of the church’s chapel doors, he held hands with his wife and three children, according to a video taken by Juntos, an immigrant rights group. A crowd of supporters chanted a version of their usual rallying cry, “sí se puede,” which means, “yes we can.”

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“Sí se pudo,” the crowd shouted. “Yes, we did it.”

Before seeking sanctuary, Flores had been an arborist, trimming trees for a living in the Philadelphia area. “I have always worked outdoors,” he said, “and I have never spent so much time locked up.”

Asked how it felt to breathe the air outside, he responded with a smile. “Wow,” he said. “It’s impressive.”

Deportations from the interior of the United States, not just those at the border, have risen under President Trump. From Jan. 22 to Sept. 9, officials deported nearly 54,000 immigrants from the interior, a 34 percent increase over the same period last year, and said they expect the numbers to climb, as The Washington Post has reported.

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According to Immigration and Customs Enforcement policy, agents generally avoid arresting immigrants at churches, schools and hospitals. As a result, hundreds of churches around the country have provided refuge to undocumented immigrants at risk of immediate deportation.

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This week alone, churches in New Jersey and Connecticut have offered sanctuary to undocumented immigrants. A 68-year-old former Fulbright scholar sought refuge at a church in Meriden, Conn., to avert an imminent deportation to his native Indonesia, the Associated Press reported. An Indonesian Christian couple said to have fled religious persecution took sanctuary in a church in Highland Park, N.J., the Ashbury Park Press reported. And a Mexican woman left a North Carolina church for the first time since June, after a judge vacated her deportation order, according to the AP.

The Flores case provides momentum for other refugees seeking sanctuary, in limbo, his supporters said.

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“This is a day to celebrate freedom,” Erika Almiron, executive director of Juntos, said Wednesday. “It means freedom for every community member that is afraid at this moment.”

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While Flores, 40, has been living in Philadelphia since 1997, he has been arrested multiple times for reentering the country illegally. In 2015, immigration agents arrested him in a raid at his home, in front of his children, and sent him to Pike County Correctional Facility for 16 months, according to Juntos’s website.

Flores’s daughter, Adamaris, spoke to ABC News about how the detention affected her.

“I didn’t know if they were going to send him to Mexico or if I was ever going to see him again,” Adamaris told ABC News. “I had trouble in school. My mom sometimes didn’t even want to come out of her room.”

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The day before he was scheduled to be deported, 90 days after he was released from detention, Flores took sanctuary in the church. Spending 11 months in the church, Flores said Wednesday, “every day is the same, you’re in the same place.”

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“It’s very difficult to see people walking outside with their families, with their children, and not being able to do that,” he said, according to the video. But the solitude was worth it, he said, for his family.

“You have to keep fighting,” he said. “Because after the storm comes the calm.”

What allowed him to apply for a visa goes back to one day in 2004, when Javier was attacked and stabbed with box cutters in Bensalem, Pa., according to a police report cited by ABC News. Because he worked with law enforcement to locate and arrest his assailants, Flores was made eligible for a special visa for victims of certain crimes who cooperate with police, his lawyer, Brennan Gian-Grasso said.

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While his visa application was filed in 2015, Flores required a specific waiver because of the illegal re-entries on his record. After two denials and appeals, Flores’s lawyer finally obtained the waiver last week.

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It will likely take about another year for the visa to be finalized, Gian-Grasso said, because of a major backlog of cases. Afterward, he will be able to file for permanent residency, his lawyer said. In the meantime, Flores is protected from deportation, Gian-Grasso said.

After leaving the church, advocates from Juntos planned to take Flores to get his ankle monitor removed, Almiron said. Then, the father planned to go home and run and play with his children. Most importantly, he hoped to find a job to support his family again, he said.

Asked what he hoped to have for dinner that night, Flores’s wife, Alma Lopez Mendoza, responded for him.

“I’m hoping that he takes me out,” she said.