By Hannah Rabinowitz, Devan Cole, Katelyn Polantz and Evan Perez

(CNN) — Kilmar Abrego Garcia, the Maryland man mistakenly deported to El Salvador in March, has been returned to the United States to face federal criminal charges, Attorney General Pam Bondi said Friday.

For months, the Trump administration has been locked in an intense standoff with the federal judiciary over court orders for the government to “facilitate” Abrego Garcia’s return from El Salvador, where he was mistakenly deported in mid-March, in a situation that one federal judge warned could present an “incipient crisis” between the two branches.

Abrego Garcia has been indicted on two criminal counts in the Middle District of Tennessee: conspiracy to unlawfully transport illegal aliens for financial gain and unlawful transportation of illegal aliens for financial gain.

The indictment unsealed Friday afternoon accuses Abrego Garcia and others of partaking in a conspiracy in recent years in which they “knowingly and unlawfully transported thousands of undocumented aliens who had no authorization to be present in the United States, and many of whom were MS-13 members and associates.”

Abrego Garcia and his family say he fled gang violence in El Salvador and have denied allegations he’s associated with MS-13.

The White House signed off on the decision to return Abrego Garcia to the US to face criminal charges, sources familiar with the matter told CNN. The decision to return Abrego Garcia was made in the last few days, the sources said. The State Department was also involved in the decision-making, one of the sources said.

However, President Donald Trump on Friday praised Bondi and the Justice Department for Abrego Garcia’s return, and he said it was the department’s decision to bring him back.

“He should have never had to be returned, take a look at what’s happened with it. Take a look at what they found in the grand jury,” the president told reporters aboard Air Force One. “I thought Pam Bondi did a great job.”

While Trump administration officials pointed to the charges as justifying their effort to remove Abrego Garcia from the United States, the decision to prosecute prompted the resignation of the chief of the Justice Department’s criminal division in Nashville, people briefed on the matter told CNN.

Simon Sandoval-Moshenberg, an attorney for Abrego Garcia, accused the Trump administration of “playing games” with the legal system and said his client should appear in immigration court, not criminal court.

“The government disappeared Kilmar to a foreign prison in violation of a court order. Now, after months of delay and secrecy, they’re bringing him back, not to correct their error but to prosecute him. This shows that they were playing games with the court all along,” Sandoval-Moshenberg said in a statement to CNN. “Due process means the chance to defend yourself before you’re punished, not after. This is an abuse of power, not justice.”

ABC News first reported that Abrego Garcia was en route to the US.

Indictment alleges trafficking conspiracy

“Abrego Garcia has landed in the United States to face justice,” Bondi said as she announced the charges at a news conference on Friday. She thanked Salvadoran President Nayib Bukele for agreeing to return Abrego Garcia to the US to face prosecution.

The allegations date back to 2016 and involve a half-dozen alleged unnamed co-conspirators, with one, identified as CC-6 of Guatemala, described as being a “primary sources of supply of undocumented aliens for the conspiracy.”

The conspiracy allegations outline how, over the years, Abrego Garcia and others worked to move undocumented aliens between Texas and Maryland and other states more than 100 times.

Working with another co-conspirator, referred to as CC-1, Abrego Garcia and that unnamed individual “ordinarily picked up the undocumented aliens in the Houston, Texas area after the aliens had unlawfully crossed the Southern border of the United States from Mexico,” the indictment said.

The two “then transported the undocumented aliens from Texas to other parts of the United States to further the aliens’ unlawful presence in the United States.”

Prosecutors said in the indictment that to cover up the alleged conspiracy, Abrego Garcia and his co-conspirators “routinely devised and employed knowingly false cover stories to provide to law enforcement if they were stopped during a transport,” including claims that the migrants being transported were headed to construction jobs.

Though prosecutors portrayed Abrego Garcia as being central to a crime-driven conspiracy, they did not describe him as the mastermind of the yearslong plot. Instead, he’s identified as just one part of a sprawling conspiracy that was led by an unnamed co-conspirator.

His conspiracy charges specifically relate to a trip in November 2022 where Abrego Garcia is accused of driving a Chevrolet Suburban and was pulled over on a Tennessee interstate highway, with nine other Hispanic male passengers who didn’t have any identification or luggage.

The indictment also describes the co-conspirator CC-1 as being part of an alleged scheme of transferring money alongside Abrego Garcia. Another co-conspirator, CC-2, is alleged with Abrego Garcia and another co-conspirator to have managed the cell phones of undocumented aliens “to ensure (they) could not and would not contact anyone else during the trip” within the US.

Prosecutors allege that Abrego Garcia also transported narcotics to Maryland, though he wasn’t charged with any crimes related to illegal drugs.

Federal Magistrate Judge Barbara Holmes in Nashville, Tennessee, determined that Abrego Garcia will be held in custody until at least next Friday, when there will be an arraignment and detention hearing, the Associated Press reported.

Abrego Garcia appeared in court wearing a short-sleeved, white, button-down shirt, according to the AP. When asked if he understood the charges, he told the judge: “Sí. Lo entiendo.” An interpreter then said: “Yes. I understand.”

Chief of DOJ criminal division in Nashville resigned over the case

The chief of Justice Department’s criminal division in Nashville resigned over the decision to charge Abrego Garcia, people briefed on the matter said.

The Justice Department’s push to pursue human trafficking charges against Abrego Garcia had caused some disagreement among prosecutors in the Nashville US attorney’s office, sources said.

Ben Schrader, the chief of the criminal division in the US Attorney’s Office for the Middle District of Tennessee, resigned the same week of the grand jury indictment last month.

He posted a message on LinkedIn, which did not mention the Abrego Garcia case, saying he had resigned after nearly 15 years. Schrader added, “It has been an incredible privilege to serve as a prosecutor with the Department of Justice, where the only job description I’ve ever known is to do the right thing, in the right way, for the right reasons.”

Schrader, the Nashville US attorney’s office and the Justice Department headquarters declined comment to CNN.

A US official pointed CNN to the seriousness of the allegations in the indictment and said the administration’s priority to pursue immigration enforcement means that anyone who didn’t want to be a part of the use priorities can leave.

Democratic lawmakers continue to criticize administration

Democratic lawmakers celebrated Abrego Garcia’s return, while criticizing the Trump administration for deporting him in the first place and denying due process.

“As I have repeatedly said, this is not about the man, it’s about his constitutional rights – and the rights of all. The Administration will now have to make its case in the court of law, as it should have all along,” said Maryland Sen. Chris Van Hollen, who met with Abrego Garcia in El Salvador earlier this year.

Florida Rep. Maxwell Frost said constitutional rights “are not subject to the whims of any president, past or present.”

Rep. Pramila Jayapal of Washington said, “Mr. Abrego Garcia was kidnapped in front of his young child, and disappeared to El Salvador with no due process,” referring to the March traffic stop during which Abrego Gacia was taken into custody while his son was in the car.

Republican members of Congress have commented publicly, but Secretary of State Marco Rubio thanked Bukele and Bondi in a Friday post on X, saying Abrego Garcia’s can now “face justice for his crimes.”

Standoff between Trump and judiciary

Abrego Garcia was mistakenly deported in March to El Salvador due to an “administrative error,” according to an Immigration and Customs Enforcement official. He was sent to the country’s notorious mega-prison where he was held for weeks before being moved to another facility.

The case became a political lightning rod for the Trump administration and its deportation program, while Trump’s shifting rhetoric about whether he could return the Maryland father had raised questions about the administration’s willingness to comply with the courts.

But the administration’s initial acknowledgement in a court filing that it mistakenly deported him opened it up to heightened scrutiny, even among Republicans otherwise supportive of Trump’s agenda.

Across the aisle, Van Hollen drew headlines when he visited Abrego Garcia in El Salvador, but his party has debated how much to embrace the Salvadoran national’s removal and the due process argument as a rallying cry of opposition to the administration.

Trump had said this spring that he could secure Abrego Garcia’s return – contradicting previous remarks made by him and his top aides who said the US did not have the ability to bring him back because he was in the custody of a foreign government, despite the Supreme Court ruling that the Trump administration must “facilitate” his return.

The administration’s posture and legal arguments in the case had consistently frustrated both conservative and liberal jurists alike, who raised alarm bells about officials’ apparent disregard for due process rights given their cavalier response to the deportation, which several different administration lawyers described as an “administrative error” that they were powerless to rectify.

In April, for instance, Bondi insisted that Abrego Garcia “is not coming back to our country.”

Bukele and Trump previously made clear during an April Oval Office meeting that Abrego Garcia would not be returned to the US. But on Friday, he said in a post on X: “We work with the Trump administration, and if they request the return of a gang member to face charges, of course we wouldn’t refuse.”

US District Judge Paula Xinis has allowed a fact-finding process to unfold so she can figure out what the government has been doing to comply with her directive that officials bring Abrego Garcia back to the US. But the case largely faded into the background in recent weeks as that discovery process has dragged on mostly out of public view.

In the Maryland case, the Justice Department told the judge on Friday that they had complied with her order to bring Abrego Garcia back to the US, in a bid to end the political standoff that had put pressure on administration attorneys in court.

“Abrego Garcia was returned to the United States today, to stand trial on criminal charges in the Middle District of Tennessee. Considering this development, the Court’s preliminary injunction should be dissolved, and the underlying case should be dismissed as moot,” DOJ attorneys wrote in a brief filing.

Judge had barred Abrego Garcia’s removal

Abrego Garcia’s return is far from a guarantee that he will remain in the US long-term. The administration’s decision to deport him to El Salvador violated a 2019 order from a judge that said he could not be deported to his home country because of fears that he would face gang violence.

That mandate, however, did not preclude the government from removing him to a third country. Officials have previously said if he were returned to the US, they may deport him to another country or attempt to wipe away the 2019 order.

Abrego Garica’s case this year went all the way to the Supreme Court, where the justices in April required the administration to “facilitate” his return but not “effectuate” it. That somewhat cryptic language allowed the administration to claim a victory for weeks as Abrego Garcia remained in detention.

The Supreme Court did not give the administration a deadline for when Abrego Garcia should be returned. The opinion was unsigned and no dissents were noted.

As the Trump administration continues its aggressive crackdown on immigration, it has been accused of wrongly deporting at least two other men. Earlier this week, one of the men — a Guatemalan national who was hastily deported to Mexico — was returned to the US.

This story has been updated with additional reporting.

CNN’s Kaitlan Collins and Priscilla Alvarez contributed to this report.

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