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President Obama's new programs that could protect millions of undocumented immigrants from deportation have been put on hold.

A Texas judge issued an injunction Monday temporarily stopping the plan from taking effect. That means the government cannot accept applications from hundreds of thousands of young undocumented immigrants who were newly eligible for deportation relief starting Wednesday.

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But the decision is just the beginning of what is likely to be a long, messy legal battle over the president's executive actions on immigration.

Legally speaking, what happens now?

The Department of Justice will appeal the decision by U.S. District Court Judge Andrew S. Hanen, according to the White House.

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"The law is on our side and history is on our side," Obama said Tuesday. "This is not the first time where a lower court judge has blocked something or attempted to block something that ultimately is going to be lawful."

At the same time, advocates who support the president's programs want the Justice Department to request an emergency stay, which would suspend Hanen's injunction and allow the plan to move forward. If the department does request a stay, the Fifth Circuit Court of Appeals (a higher court) would rule on it.

The White House said Tuesday, however, that no decisions have been made on whether to seek a stay. The Justice Department will decide in the "next couple of days" on taking legal action beyond an appeal, including a stay, White House domestic policy director Cecilia Muñoz told reporters on a conference call.

How would a stay affect Obama's immigration programs?

If the administration asks for a stay and Fifth Circuit grants its request, the government could begin accepting and processing applications for deportation relief and work permits. But if they don't, the program would remain on hold.

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Advocates expect the Fifth Circuit to rule on a stay within weeks if the government does make an emergency request. The Fifth Circuit is known to have a conservative bent, but activists believe it will side with the Obama administration.

"We are confident Judge Hanen's decision will be overturned," Melissa Crow, legal director of the American Immigration Council, told reporters on a conference call Tuesday.

Debbie Smith, associate general counsel for the Service Employees International Union, described Monday's decision as a "bump in the road."

"It's not the end of the game and we believe justice will prevail," she said.

If the court issues a stay, is that the end of it?

No. The Fifth Circuit would still have to consider the appeal of Hanen's injunction and that process could take months.

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If the Fifth Circuit ultimately denies the government's appeal, Obama's programs could shut down again even if the stay is granted in the next few weeks.

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Hanen still must make a ruling on the merits of the lawsuit; whether Obama's executive actions on immigration violated the Constitution. Advocates expect the losing side to appeal to the Fifth Circuit, and whoever loses there to request a Supreme Court review.

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The bottom line is: the legal wrangling could go on for months without a final resolution.

How are activists responding?

Meanwhile, immigrant-rights activists are plowing ahead with information sessions and outreach efforts tied to the stalled deportation relief programs.

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The White House and its supporters are confident the legal system will validate the president's programs and they don't want Hanen's decision to scare potential applicants from seeking deportation relief.

“Regardless of today’s ruling, we are urging the hundreds of thousands of immigrants across our region that [qualify] to continue to collect their documents and become prepared for the moment when this temporary decision is overturned,” said Gustavo Torres, executive director of CASA, a group advocating for immigrant workers.

Advocates are holding more than 75 events nationwide this week promoting Obama's programs, according to the Alliance for Citizenship. They include information sessions and clinics explaining what the decision means and encouraging people to continue to collect the documentation they need to apply.

The second, larger portion of Obama's immigration program — intended for parents of U.S. citizens and permanent residents — was set to begin in mid-to-late May. But the Department of Homeland Security said in a statement it is halting preparations for Obama's new deportation-relief initiatives.

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Homeland Security Secretary Jeh Johnson said he disagrees with Hanen's ruling, but "we recognize we must comply with it."

While advocates brushed off Monday's court decision, Republicans hailed it as a significant victory.

"Today's ruling reinforces what I and many others have been saying for a long time: that President Obama acted outside the law when he went around Congress to unilaterally change our nation's immigration laws," Texas Sen. John Cornyn (R) said in a statement.

Ted Hesson contributed reporting.

This post was updated to include comments from President Obama and White House officials.

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Jordan Fabian is Fusion's politics editor, writing about campaigns, Congress, immigration, and more. When he's not working, you can find him at the ice rink or at home with his wife, Melissa.