WASHINGTON – A federal judge on Thursday sentenced Roger Stone, a longtime friend of President Donald Trump’s, to three years and four months in prison for impeding a congressional investigation of Russian interference in the 2016 U.S. presidential election.

The penalty from U.S. District Judge Amy Berman Jackson comes after weeks of infighting over the politically charged case that threw the Justice Department into crisis, and it is probably not the final word. Even before the sentencing hearing, Trump seemed to suggest on Twitter that he might pardon Stone. With the proceedings ongoing, Trump questioned whether his ally was being treated fairly.

In a lengthy speech before imposing the penalty, Jackson seemed to take aim at Trump – saying Stone “was not prosecuted for standing up for the president; he was prosecuted for covering up for the president” – and Attorney General William Barr, whose intervention to reduce career prosecutors’ sentencing recommendation she called “unprecedented.” But she said the politics surrounding the case had not influenced her final decision.

“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 foundations of our democracies. If it goes unpunished it will not be a victory for one political party; everyone loses.”

She added, “The dismay and disgust at the defendant’s belligerence should transcend party.”

Prosecutors and defense attorneys traded barbs in court Thursday over the penalty Stone should face, and the judge sought both to understand their disputes and the internal Justice Department haggling over what penalty the government would endorse. The judge also made clear that she thought Stone had not been unfairly targeted.

“He was not prosecuted by anyone to gain political advantage,” she said.

A little more than an hour earlier, Trump publicly insisted the opposite. In a tweet, he compared Stone to former FBI director James Comey, former FBI deputy director Andrew McCabe and former secretary of state Hillary Clinton, for whom the president has advocated charges.

” ‘They say Roger Stone lied to Congress.’ @CNN,” Trump tweeted, tagging the news network. “OH, I see, but so did Comey (and he also leaked classified information, for which almost everyone, other than Crooked Hillary Clinton, goes to jail for a long time), and so did Andy McCabe, who also lied to the FBI! FAIRNESS?”

Prosecutors took a fairly aggressive posture toward Stone. Those in court Thursday were not the four prosecutors previously assigned to the case; they quit over a dispute about what penalty the Justice Department should recommend. The new prosecutors in court adopted the same technical arguments of their predecessors early in the proceedings, and defended the Justice Department’s bringing the case.

“This prosecution is righteous,” Assistant U.S. Attorney John Crabb said.

Crabb said the court “should impose a substantial period of incarceration,” though he did not propose a specific number of months or years. “The court will rely on its own sound judgment and experience,” he said. The previous prosecutors had recommended that Stone spend seven-to-nine years in prison.

Jackson made clear that she thought Stone’s crimes were serious. She called his testimony “plainly false” and “a flat-out lie,” and said his misdirection “shut out important avenues” for Congress to investigate. She said Stone knew “it could reflect badly on the president if someone learned” about his efforts to obtain damaging information about Clinton, who was then running against Trump to be president, from the anti-secrecy group WikiLeaks.

Jackson acknowledged the unusual politics surrounding situation as the hearing began, saying she had reviewed two sentencing memorandums filed by the government. The first, filed by career prosecutors initially assigned to the case, recommended a term of seven to nine years. The second, filed after Barr personally intervened just hours after Trump tweeted about the case, recommended something lesser.

Jackson noted that prosecutors’ “initial memo has not been withdrawn,” and suggested that the government’s updated position was somewhat unusual.

“For those who woke up last week and became persuaded that the guidelines are harsh and perhaps sentences shouldn’t be driven by strict application of a mathematical formula . . . I can assure you that defense attorneys and judges have been making that argument for a very long time,” she said. “But we don’t usually succeed in getting the government to agree.”

Jackson pressed Crabb for answers. She asked why the Justice Department ultimately chose to recommend bucking the guidelines in the case – when department policies do not let prosecutors argue for a sentence below the guidelines without approval – and questioned why Crabb was in court at all.

“I fear that you know less about this case than possibly anybody else in the courtroom,” Jackson said.

Crabb said that the original prosecutors on the case had approval from the U.S. attorney to make the recommendation they did, and that their filing was “done in good faith.” He said his understanding was that there had been a “miscommunication between the attorney general and the U.S. attorney for the District of Columbia,” centered around “what the expectations were from the AG and what the appropriate filing would be.” He apologized for the “confusion” – though even in court, his position seemed somewhat muddled.

Crabb seemed to endorse the same technical logic prosecutors had used in generating their recommendation in the first sentencing memorandum. Asked by Jackson about the change in position, Crabb said, “The guidelines enhancement applies here for the reasons set forth in the original sentencing memorandum.” He did not elaborate.

“What is the government’s position today?” Jackson asked, emphasizing the word today. When Crabb said he had nothing more to offer, she said with a bit of exasperation, “OK, fine.”

Stone, 67, who wore a wide-striped suit and a polka-dot tie to court Thursday, was convicted by a federal jury in November on seven counts of lying to Congress and tampering with a witness about his efforts to learn about hacked Democratic emails related to Clinton.

Prosecutors said the longtime GOP operative lied during testimony to the House Intelligence Committee in September 2017 to conceal his central role in the Trump campaign’s efforts to learn about computer files hacked by Russia and made public by anti-secrecy group WikiLeaks. Stone also threatened a witness who was an associate of his in an attempt to prevent the man from cooperating with lawmakers.

Stone was the sixth Trump associate convicted and the last person indicted in special counsel Robert Mueller’s investigation.

Trump injected additional drama into Stone’s sentencing day with an overnight tweet that hinted he could issue a pardon to Stone.

“President Trump could end this travesty in an instant with a pardon, and there are indications tonight that he will do that,” Fox News host Tucker Carlson said in a video shared by Trump with his Twitter followers. Carlson noted in the video a series of pardons and commutations that the president has already granted this week.

Carlson called Stone’s prosecution “wholly political” and “a shocking insult to the American tradition of equal justice.” Trump, who spent the night in Las Vegas, fired off the tweet shortly before 2 a.m. Eastern time.

Stone’s defense attorneys have asked for probation, citing his age and lack of criminal history. On Friday, Stone also requested a new trial after Trump suggested that the forewoman in Stone’s case had “significant bias.”

Defense attorney Seth Ginsberg requested mercy in court Thursday, saying Stone is “a real person, not a media figure, not a political character but a real person,” who is soon to be a great-grandfather. He emphasized that Stone has “given of himself” to various causes – including veterans, animal welfare and football players suffering from traumatic brain injuries – and has “worked to bridge racial divides in this country.”

That, he said, is “who Mr. Stone really is – not the larger than life political persona that he plays on TV, but the real person who goes home every day to his wife and his family.”

Ginsberg argued that New York City comedian and radio host Randy Credico, the witness Stone was convicted of threatening, understood Stone was “all bark and no bite.” Credico appealed for leniency in a letter to the court: “The bottom line is Mr. Stone, at his core, is an insecure person who craves and recklessly pursues attention . . . Prison is no remedy.”

“Even though the words on their face could be read as threatening, in the context of the dialogue between Mr. Credico and Mr. Stone it’s our position that these words . . . did not themselves constitute a threat as all,” Ginsberg said. “Mr. Stone is known for using rough, provocative, hyperbolic language. Mr. Credico knew that . . . in the context of that private conversation Mr. Credico understood that it was just Stone being Stone, he’s all bark no bite. . . . there’s no threat at all.”

Crabb countered that the government believes the enhancement for threatening violence should apply: “The fact is that the defendant threatened Mr. Credico’s personal safety and his pet,” Crabb said. The judge agreed, quoting from some of Stone’s profane texts to Credico.

“The defendant referred to this as banter, which it hardly is,” the judge said.

Jackson said this week that she will postpone the implementation of Stone’s sentence while she weighs whether he deserves a new trial.

Crabb spoke briefly in favor of a sentencing enhancement for successful obstruction of justice, noting that both government filings were in concert on that point.

That is technically true, though the memorandum he signed suggested the enhancement was duplicative and added, “it is unclear to what extent the defendant’s obstructive conduct actually prejudiced the government at trial.”

The judge ultimately applied the enhancement, saying Stone’s lies led to an “incorrect inaccurate and incomplete report” from Congress.

Crabb also argued for an enhancement for extensive obstructive conduct, saying Stone engaged in a “series of lies” and destroyed records – though the judge rejected that.

Front-line prosecutors initially said a seven-to-nine-year prison term for Stone “will send the message . . . that [impeding] a congressional investigation on matters of critical national importance are not crimes to be taken lightly.”

Prosecutors also said that after Stone’s “crimes were revealed by the indictment in this case, he displayed contempt for this Court and the rule of law.”

But the four trial prosecutors quit the case last week when the Justice Department undercut the initial sentencing recommendation and suggested that three to four years was “more typical” in cases like Stone’s.

In its subsequent request, the government said that while the higher sentencing guidelines technically apply because Stone threatened violence against a witness, they should be set aside because the witness now states he did not feel that Stone would personally and directly harm him.

Given Stone’s age, health and status as a first-time offender, the higher sentencing range “could be considered excessive and unwarranted under the circumstances,” the government’s amended request said.

The new sentencing recommendation came after the president tweeted that the initial suggested penalty for his friend was “horrible and very unfair.”

The Trump administration’s intervention in Stone’s case has set off a crisis for the Justice Department, which has been accused of suggesting a more lenient sentence for Stone to appease the president.

Amid accusations impugning the independence of the Justice Department, Barr stated publicly that the president’s attacks against judges, prosecutors, jurors and his aides “make it impossible for me to do my job and to assure the courts . . . and the department that we’re doing our work with integrity.” This week, those close to Barr said the attorney general has told Trump advisers he has considered resigning over the president’s tweets. Trump, meanwhile, has continued to tweet about the Stone case – suggesting his friend deserves a new trial – even as the Justice Department, with Barr’s blessing, has opposed Stone’s request on that front.

Lawyers for Stone argue he deserves no jail time, saying federal guidelines would call for a sentence of 15 to 21 months for a first offense without aggravating factors.

Citing Stone’s loss of professional standing and hardships, defense attorneys Bruce Rogow, Robert Buschel and Grant Smith wrote, “no one could seriously contend that a [reduced] . . . sentence would cause anyone to walk away from these proceedings believing that one can commit the offenses at issue here with impunity.”

Stone is one of several Trump advisers and confidants who have either been convicted or pleaded guilty in connection with the special counsel probe. That list includes former Trump campaign chairman Paul Manafort, former deputy campaign chairman Rick Gates, former national security adviser Michael Flynn, former Trump lawyer Michael Cohen and former campaign adviser George Papadopoulos.

Stone’s two-week trial in November refocused attention on the Trump campaign’s keen appetite for dirt on its political opponents. The trial included testimony from former 2016 deputy campaign manager Gates, who testified that he overheard a July 2016 phone call in which Trump himself seemed to discuss WikiLeaks with Stone.

The trial also highlighted Trump’s ongoing standoff with congressional Democrats, then conducting an impeachment inquiry into whether the president pressured Ukraine to bolster his 2020 reelection bid. Trump directed the White House to withhold documents and block testimony in the inquiry, which ended in a Senate acquittal.

Prosecutors asserted at trial that Stone thwarted Congress because the truth would have “looked terrible” for Trump and the campaign. Prosecutors argued Stone lied to protect the president from embarrassment.

Prosecution witnesses included Gates and Trump campaign strategist Steve Bannon, who took over in August 2016 when Gates’s boss, Manafort, was fired over his Ukraine ties. Gates and Bannon said the campaign viewed Stone as a sort of liaison to WikiLeaks who claimed – even before the Russian hacking was known – to have insight into its plans.

Stone’s attorneys repeated his position that there was “no collusion” with Russia and portrayed their client as a hapless victim of the same braggadocio and chicanery that he practiced on others, burnishing his reputation as a political dirty trickster. Stone’s defense said any of their client’s misstatements were inconsequential and never amounted to anything.

Prosecutors argued that Stone’s communications with conservative writer Jerome Corsi described plans during the campaign to contact WikiLeaks founder Julian Assange, who had been living under house arrest at the Ecuadoran Embassy in London since 2012.

Stone and Corsi, who was never charged, denied having contact with WikiLeaks, saying prosecutors were guessing based on Assange’s public statements.

Jackson also will consider whether to punish Stone for repeatedly violating a court gag order.

Before trial, Stone posted a photo of Jackson with an image of crosshairs next to her head on Instagram in February 2019. During his trial, he appealed for a presidential pardon through Alex Jones, a noted conspiracy theorist who hosts the right-wing website Infowars, prosecutors said.

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The Washington Post’s John Wagner contributed to this report.