Refugees and immigrants from countries that the Trump administration has listed as security concerns who arrived in the US after Friday evening are still in limbo.

There were protests at airports across the country Saturday. Meanwhile, a federal judge blocked a portion of Trump's directive in an emergency hearing in Brooklyn. The court ordered that refugees and immigrants with legal documents to enter the US not be returned to their home countries. It effectively paused the program, without ending it.

The judge’s order cites the danger these immigrants would face if returned, and the potential of a violation of their due process rights, the constitutional guarantee of fair treatment under the law. The judge did not, however, order that they be released from government custody, nor did she rule on the constitutionality of the executive order itself.

The decision prevents federal agencies “from, in any manner or by any means, removing individuals with refugee applications approved by US Citizenship and Immigration Services as part of the US Refugee Admissions Program, holders of valid immigrant and non-immigrant visas, and other individuals from Iraq, Syria, Iran, Sudan, Libya, Somalia, and Yemen legally authorized to enter the United States.”

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Luis Mancheno, an immigration attorney and fellow at the Benjamin N. Cardozo School of Law, which represents one of the unnamed petitioners to the lawsuit, says that the judge’s language was strong. In court, Mancheno says, she said, “Nobody is to be removed.”

The order came just in time for his organization’s client, who was scheduled to be deported at 9:30 p.m. Saturday.

It is unclear how many people are being detained at airports across the country, but advocacy organizations estimate hundreds of people with valid travel documents are in federal custody. Mancheno says the judge asked how many people have been detained but the attorney representing the government did not know. Mancheno himself fled violence in Ecuador to find safety in the US and says that had the US government turned him away at the airport, he would have been killed.

PRI has asked the Department of Justice for details about the detentions that have occurred since Trump signed his executive order on Friday evening. The justice department has not responded.

At San Francisco International Airport, as the order came down, protesters chanted, “Let them out! Let them out!” Organizers of the protest there believe there are two people from Yemen and three from Iran in custody at that airport, but like the government attorney, couldn’t say for sure. One of them, an 80-year-old Iranian man in a wheelchair with legal permanent resident status, was released at 7 p.m., according to reporters and organizers.

Eighty-year old Iranian who landed 6 hours ago was just let out says: "Trump is America's Ahmadinejad" pic.twitter.com/yc7iO8B9FV — Sana Saleem (@sanasaleem) January 29, 2017

The executive order that Trump signed Friday gave federal agencies broad power to detain or deny entry to anyone arriving as a refugee from any country or as an immigrant of any kind from the so-called “countries of concern.” Late in the day, the State Department said this includes people holding dual-citizenship from a country of concern and another country that is not the US.

Elica Vafaie, a lawyer with nonprofit Asian Americans Advancing Justice, was at SFO Saturday. She said she was gathering the names of Iranian Americans who came through the airport but were not detained to find out what agents were asking while vetting them. This kind of questioning, she says, was another matter not addressed in Saturday’s emergency hearings.

“We were operating in a legal world where legal permanent residents have much more rights than what was written in that executive order. So we’re kind of seeing what these new practices are in the first week of this new administration,” Vafaie said.

Zahra Billoo of the Council on American Islamic Relations Bay Area chapter said her organization too is getting ready for a fight.

“We don’t know how the Trump administration will fight back,” she said. “What we are advising people is that if they have a valid visa or if they are a legal permanent resident outside of the country, particularly from the seven Muslim-majority countries that are being targeted, you should return immediately.”

She also advised that travelers coming to the US from these seven countries should be in touch with lawyers before they return. She and others, she said, will stay at the airport until all the detained immigrants are safe, she said.

Hundreds came to John Fitzgerald Kennedy airport in New York Saturday, where 12 refugees en route to a new life in the US were detained. They chanted, “Build the wall, we’ll tear it down” and, “No hate, no fear, refugees are welcomed here!”

“I’m here today because this Muslim ban is against America’s ideals,” said Justin Hendrix, a father from Brooklyn. “America has always stood for welcoming immigrants, refugees, the vulnerable and yesterday’s executive order flies in the face of everything this country is about.”

When he saw news of the protest on social media, he got in his car and decided to be part of it.

Kazi Fouzia, part of the community organization Desis Rising Up and Moving, offered Islamic prayers as reporters and onlookers recorded the moment.

Joshua Stephens, a writer, said, “People talk about what they would have done if they were around in Nazi Germany and this is our moment to do what people should have done.“

A diverse group, including many parents with young children, joined a national swell of protest at airports around the country, including Boston Logan, Washington Dulles and Minneapolis St. Paul, in addition to SFO and JFK. At Kennedy Airport, they gathered at terminal 4, where at least some of the refugees were being held.

Hameed Khalid Darweesh, 53, and Haider Sameer Abdulkhaleq Alshawi, 33, two Iraqis who filed the lawsuit for themselves and others in similar situations, were released from the New York airport before the emergency hearing Saturday.

Immigration ban not sitting well with America. pic.twitter.com/PV6NQZml10 — ian bremmer (@ianbremmer) January 29, 2017

Daniel Altschuler of Make the Road NY, an immigrant rights organization that helped organize the New York protest, says the day had two sides. “It is a dark moment where families are being separated. There’s a moral crisis in this country. At the same time, we’re seeing an incredible response from the community.”

Earlier on Saturday, Trump told reporters that his executive order was working well.

“It’s not a Muslim ban, but we were totally prepared. It’s working out very nicely. You see it at the airports, you see it all over,” he said, according to a White House press pool report.