A federal judge on Thursday sentenced Roger Stone Roger Jason StoneOur Constitution is under attack by Attorney General William Barr Justice IG investigating Stone sentencing: report Romney says Trump's protest tweets 'clearly intended to further inflame racial tensions' MORE to three years and four months in prison for lying to Congress and witness tampering, and criticized President Trump Donald John TrumpObama calls on Senate not to fill Ginsburg's vacancy until after election Planned Parenthood: 'The fate of our rights' depends on Ginsburg replacement Progressive group to spend M in ad campaign on Supreme Court vacancy MORE for trying to influence the outcome of the case over his former adviser.

Thursday's sentencing hearing follows a tumultuous stretch that saw Trump attack the original prosecutors, the judge and the jury in the case on behalf of his longtime adviser. And it follows the withdrawal of the original prosecution team from the case after the Justice Department amended their recommendation that Stone serve seven to nine years in prison.

Judge Amy Berman Jackson, an Obama appointee on the U.S. District Court for the District of Columbia, delivered an implicit rebuke to Trump over his comments about the case and admonished the administration for its reversal over the past week.

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"This case also exemplifies why it is that this system, for good reason, demands that the responsibility [for sentencing] falls on someone neutral," Jackson said. "Someone whose job may involve issuing opinions in favor of and against the same administration in the same week. Not someone who has a longstanding friendship with the defendant. Not someone whose political career was aided by the defendant. And surely not someone whose personal involvement underlined the case."

"The court cannot be influenced by those comments," she went on. "They were entirely inappropriate. But I will not hold them against the defendant, either."

Stone, wearing a pinstripe black suit with a blue tie, largely didn't react to the sentence has he stood before the courtroom. He will also have to pay a $20,000 fine, and serve two years of supervised release after his prison term.

Stone later donned a black hat and entered a waiting car without answering questions from reporters as groups of opposing demonstrators outside the courthouse called for his pardon or for him to be locked up. Also at the courthouse was former Breitbart pundit Milo Yiannopolous, who also attended Stone's trial.

Stone's legal saga is still not completely over. His lawyers asked Jackson for a new trial in a sealed motion submitted last week. Jackson said that Stone's sentence will be delayed from going into effect until after that motion is settled.

The president weighed in Thursday during remarks at a prisoner graduation event in Las Vegas, saying Stone’s case “has not been a fair trial” but that he’s not prepared to issue a pardon yet.

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“I’m following this very closely, and I want to see it play out to its fullest because Roger has a very good chance of exoneration in my opinion,” Trump said.

“I’m not going to do anything in terms of the great powers bestowed upon a president of the United States. I want the process to play out,” he added. “I think that’s the best thing to do. Because I’d love to see Roger exonerated, and I’d love to see it happen, because I personally believe he was treated very unfairly.”

During the hearing, Jackson sharply questioned the new attorney for the prosecution, John Crabb Jr. of the D.C. U.S. Attorney's Office, over the administration's sentencing reversal.

Crabb demurred when Jackson asked whether he actually wrote the updated sentencing memo that the government submitted under his name last week or if his superiors at the Justice Department had directed him to ask for a sentence "far less" than the original recommendation. He said that he was not authorized to discuss internal department deliberations in open court.

Still, Crabb was conciliatory in his courtroom remarks, praising the original prosecution team and insisting that the Justice Department is committed to doing its job fairly.

“The Department of Justice and the United States Attorney's Office is committed to enforcing the law without fear, favor or political influence,” Crabb said. “This prosecution was — and this prosecution is — righteous.”

Despite amending the original sentencing recommendation, he argued that Stone still deserves a "substantial" prison sentence.

The move to overrule the original sentencing memo prompted a fierce backlash for the Department of Justice and Attorney General William Barr Bill BarrBarr says Ginsburg 'leaves a towering legacy' Republicans call for DOJ to prosecute Netflix executives for releasing 'Cuties' Trump doesn't offer vote of confidence for FBI director MORE, especially as Trump tweeted his support for Stone and lashed out at the team surrounding former special counsel Robert Mueller Robert (Bob) MuellerCNN's Toobin warns McCabe is in 'perilous condition' with emboldened Trump CNN anchor rips Trump over Stone while evoking Clinton-Lynch tarmac meeting The Hill's 12:30 Report: New Hampshire fallout MORE, which brought the cases against Stone as well as former Trump national security adviser Michael Flynn.

“Everything having to do with this fraudulent investigation is badly tainted and, in my opinion, should be thrown out,” Trump wrote in a series of tweets on Tuesday. “The whole deal was a total SCAM. If I wasn’t President, I’d be suing everyone all over the place. BUT MAYBE I STILL WILL. WITCH HUNT!”

Jackson called the original sentencing recommendation "thorough, well-researched and supported," but ultimately decided that a prison term of seven to nine years would be too high for Stone.

Still, she tore into Stone for his dishonesty with Congress and his repeated violations of a gag order she imposed before trial prohibiting his use of social media.

“The truth still exists, the truth still matters,” Jackson said. “Roger Stone's insistence that it doesn't, his belligerence, his pride in his own lies are a threat to our most fundamental institutions, to the very foundation of our democracy. And if it goes unpunished, it will not be a victory for one party or another.”

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The sentencing controversy has overshadowed the actual case, in which prosecutors accused Stone of lying to Congress about his contacts with associates he believed to have been communicating with WikiLeaks during the 2016 presidential campaign in an effort to feed inside information to then-candidate Trump. He was also charged with pressuring a witness into not cooperating with congressional investigators.

Prosecutors alleged during the trial that Stone lied in 2017 to the House Intelligence Committee, which was investigating Russian interference in the election, in an effort to protect the president, who was still in the early months of his administration.

“The evidence in this case will show that Roger Stone lied to the House Intelligence Committee because the truth looked bad — the truth looked bad for the Trump campaign and the truth looked bad for Donald Trump,” Aaron Zelinsky, one of the prosecutors in the case, told the jury in November.

Zelinsky and the rest of the original prosecution team withdrew from the case last week after Barr overruled their sentencing recommendation. One of the attorneys on the team resigned from the Justice Department.

The sentence is sure to increase speculation that Trump will pardon Stone. The president said publicly this week that he hasn't given it any thought, but a round of high-profile pardons and commutations this week was seen by many as a message intended for Stone and other Trump associates facing prison time.

Some lawmakers are already speaking out against the prospect of a pardon for Stone.

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"Roger Stone was found guilty of lying to Congress and threatening a witness," Rep. Adam Schiff Adam Bennett SchiffTop Democrats call for DOJ watchdog to probe Barr over possible 2020 election influence Overnight Defense: Top admiral says 'no condition' where US should conduct nuclear test 'at this time' | Intelligence chief says Congress will get some in-person election security briefings Overnight Defense: House to vote on military justice bill spurred by Vanessa Guillén death | Biden courts veterans after Trump's military controversies MORE (D-Calif.), the chairman of the House Intelligence Committee who helped lead the impeachment case against Trump, wrote on Twitter.

"He did it to cover up for Trump," Schiff continued. "His sentence is justified. It should go without saying, but to pardon Stone when his crimes were committed to protect Trump would be a breathtaking act of corruption."

— Updated at 5:06 p.m.

— John Kruzel contributed.