The Trump administration on Tuesday morning carried out the first federal execution since 2003, following a series of court battles and a Supreme Court order, released shortly after 2 a.m., clearing the way for the lethal injection to take place. 

Federal officials executed Daniel Lewis Lee, 47, who was convicted in 1999 of killing a family of three, at a penitentiary in Terre Haute, Ind. Lee was pronounced dead at 8:07 a.m. Tuesday, the Bureau of Prisons said.

“I’ve made a lot of mistakes in my life, but I’m not a murderer,” Lee said when asked if he wanted to make a final statement, according to the pool report. His final words were: “You’re killing an innocent man.”

Although the death penalty has been in decline nationwide for years, with executions and death sentences down significantly, the Justice Department has publicly pushed against that trend for nearly a year. The department has argued in court and in public statements that it needed to carry out lawful sentences, citing the gravity of the crimes involved. 

Last year, the department laid out a new lethal injection protocol — using one drug, pentobarbital — and said it would begin carrying out executions, leading to extended legal challenges. Attorney General William P. Barr had said recently that officials “owe it to the victims of these horrific crimes, and to the families left behind.” 

Lee had challenged his execution on his own and along with other death-row inmates. His execution was also opposed by some relatives of his victims, who argued against his death sentence in the case and sought to stop his lethal injection from taking place amid the coronavirus pandemic.

On Monday, Lee’s lethal injection — originally scheduled for 4 p.m. that afternoon — was left on hold following a judge’s order that he and other death-row inmates could pursue their court cases arguing that the new lethal-injection protocol is unconstitutional. 

An appeals court said late Monday that it would not let the executions take place as planned, but a divided Supreme Court weighed in overnight saying they could proceed. 

In an unsigned 5-4 order, the court’s conservative justices said the prisoners on death row had “not made the showing required to justify last-minute intervention.”

“It is our responsibility to ensure that method-of-execution challenges to lawfully issued sentences are resolved fairly and expeditiously, so that the question of capital punishment can remain with the people and their representatives, not the courts, to resolve,” said the opinion, which quoted court precedents.

Although the author is unclear, the opinion was the work of Chief Justice John G. Roberts Jr. and Justices Clarence Thomas, Samuel A. Alito Jr., Neil M. Gorsuch and Brett M. Kavanaugh.

The court’s four liberal justices wrote two dissents. Justice Sonia Sotomayor, joined by Justices Ruth Bader Ginsburg and Elena Kagan, said that the court was “hastily” ending the inmates’ challenges and that as a result, there would “be no meaningful judicial review of the grave, fact-heavy challenges” they brought.

Justice Stephen G. Breyer, joined by Ginsburg, reiterated his view that the court should examine whether the death penalty itself is unconstitutional. 

Media witnesses at Lee’s execution on Tuesday morning saw him strapped to a gurney and with an IV in his left arm and both arms restrained, according to the pool report. When the lethal drug was being injected, his breathing appeared to become labored, his chest eventually stopped moving and his lips appeared to turn blue.

Ruth Friedman, an attorney for Lee, decried the government’s decision to execute him during the coronavirus pandemic.

“It is beyond shameful that the government, in the end, carried out this execution in haste, in the middle of the night, while the country was sleeping,” she said in a statement. “We hope that upon awakening, the country will be as outraged as we are.”

Barr said that Lee had “finally faced the justice he deserved” on Tuesday morning.

“The American people have made the considered choice to permit capital punishment for the most egregious federal crimes, and justice was done today in implementing the sentence for Lee’s horrific offenses,” he said in a statement.

Even after the Supreme Court’s order, uncertainty still lingered for hours in the case. Friedman said Lee “remained strapped to a gurney” for the four hours leading up to his execution as another legal dispute played out. She said another stay was still in place.

The Justice Department said Lee would have been executed at 4 a.m., but attributed the four-hour delay that followed to his attorneys contesting whether the execution could proceed. Kerri Kupec, a department spokeswoman, called it “a last-minute procedural claim” in a statement.

Lee and another man were convicted of murdering three people, including Nancy Mueller and her 8-year-old daughter, Sarah Powell.

He and this other man, Chevie Kehoe, were part of a group intending to create a white supremacist community in the Pacific Northwest, and they traveled to Arkansas in 1996, where they robbed and murdered William Mueller, a firearms dealer, along with his wife and the child, court records show. The men placed plastic bags over their heads and threw them into a bayou, the records show.

Relatives of victims in the case had fought against Lee’s execution, asking that it be called off or at least postponed because of the coronavirus, saying they would have to put their lives at risk to witness his death.  

Lee’s execution was first scheduled to take place last year before being delayed several months by other court challenges. The victims’ relatives who spoke out said it was unfair Lee was given a death sentence while Kehoe, who officials described as the ringleader in the killings, was sentenced instead to life in prison, a position echoed later by the judge and lead prosecutor from the trial. 

In a court case filed last week, the three relatives — Earlene Peterson, Nancy Mueller’s mother; Kimma Gurel, Mueller’s sister; and Monica Veillette, her niece — had asked that the execution be postponed. Although they did not support the execution, the relatives said, they still felt obligated to attend. 

But all three said they have existing health issues, so they faced “grave risk” if they traveled during the pandemic and went to a federal prison. They asked that it be postponed so they did not have to choose between staying home or risking infection. 

“No other family should have to make this decision . . . the families of victims should not be put in a position where they have to risk their lives or give up their right” as a witness, Veillette said in an interview. “That is not how we should be treating the families of victims in this country.”

Lee’s execution had been put on hold and then cleared to proceed multiple times in recent days. A federal judge in Indiana last week blocked it from proceeding because of the relatives’ court challenge, while an appeals court panel on Sunday evening said it could take place.

The relatives ultimately decided not to travel to Indiana because they had determined that the health risks were too great. The appeals court’s ruling also came too late for them to travel as planned, they said. 

Then on Monday morning, a federal judge blocked the government from executing Lee or two other men scheduled to face lethal injections this week. Wesley Purkey, who was convicted in 2003 of raping and murdering Jennifer Long, a teenage girl, and Dustin Lee Honken, who was convicted in 2004 of killing five people, including two young girls.

Purkey’s execution is scheduled for Wednesday, although another court has temporarily stayed it on other grounds, while Honken’s is scheduled for Friday. The Justice Department is also asking the Supreme Court to let Purkey’s execution proceed, but the court has not ruled on that yet.

In a separate case, spiritual advisers for Purkey and Honken are seeking to have their executions delayed and arguing that they face health risks if they minister during the pandemic. A federal judge in Indiana denied that request Tuesday; they quickly moved to appeal.

U.S. District Judge Tanya S. Chutkan of the District of Columbia wrote in an order Monday that she was blocking all of their executions, and another set for August, because it was necessary to let the inmates’ legal challenges to the government’s lethal-injection protocol play out in court. They had argued that lethal injection is unconstitutional, saying it amounts to cruel and unusual punishment. 

The Justice Department quickly appealed to the U.S. Court of Appeals for the D.C. Circuit and the Supreme Court. Late Monday night, hours after Lee’s execution was originally scheduled, the D.C. Circuit appeals court declined to let the lethal injections proceed and said the inmates’ challenges could move forward.

In its early morning orders on Tuesday, the Supreme Court also rejected a case brought to them by the relatives of victims in Lee’s case, seeking to have his execution postponed because of their coronavirus-related fears. The court denied that without comment.

“It just became very painfully clear to us that as many times as it was said this was being done for the families of the victims ... that in the end nobody cared about us at all,” Veillette said in an interview after the execution.

She called the Supreme Court’s early morning orders disappointing but not surprising. Veillette said she was up all night monitoring the news from her home in Washington state and in regular touch with her mother, at her own home in the same state, and her grandmother in Arkansas. Early Tuesday morning, Veillette said, her attorney told her Lee had been executed.

“We will never get peace from this,” Veillette said, describing herself as deeply sad and angry at the outcome. “Because justice was not served ... This was done in Nancy and Sarah’s name. And that is the final part of their story now.”

Robert Barnes contributed to this report.