Roger Stone stood silently before the judge as she issued her sentence | Drew Angerer/Getty Images Trump ally Roger Stone sentenced to over three years in prison The case has become a flashpoint for broader concerns about political meddling in high-profile legal cases.

Roger Stone was sentenced Thursday to just more than three years in prison, a decision that raises immediate questions about whether President Donald Trump will pardon his longtime political confidant for what the president has decried as a miscarriage of justice.

U.S. District Court Judge Amy Berman Jackson handed down Stone’s 40-month sentence in a packed Washington, D.C., courtroom after spending more than two hours ticking through the twisted history of his case, which culminated last November with the GOP operative’s jury conviction on seven felony counts including lying to authorities, obstructing a congressional investigation and witness intimidation.

"The problem is nothing about this case was a joke,” Jackson said moments before sentencing Stone. “It wasn't funny. It wasn't a stunt and it wasn't a prank.”

Stone, who passed on a chance to address the courtroom, stood silently before the judge as she issued her sentence. The punishment grew in large part from the severity of his attempts to stymie the Russia probe, violations of a gag order limiting his speech during the pre-trial proceedings and for making a threat to the judge through social media.

“He was not prosecuted for standing up for the president,” Jackson added in her closing remarks. “He was prosecuted for covering up for the president.”

Jackson’s sentence for Stone — among the most severe to-date in a case originating from special counsel Robert Mueller — came a week after his potential punishment triggered a furor at the Justice Department.

Stone’s case has become a flashpoint for broader concerns about political meddling in high-profile legal cases. Trump has been using his Twitter bully pulpit to repeatedly harangue the Justice Department over its handling of the case, sparking concerns that the president influenced Attorney General Bill Barr’s decision to overrule his own prosecutors and request a lower sentence for Stone — a charge Barr denies. The situation has left many in the legal world wondering whether Trump’s refusal to scale back his public punditry, despite Barr’s own public pleas, could lead the attorney general to resign.

Jackson, an appointee of President Barack Obama, jumped at the chance to press one of the newly-assigned prosecutors, John Crabb, about the issue as he delivered the government’s final comments.

“I want to apologize to the court for the confusion the government caused with respect to sentencing,” Crabb said.

During his brief statement to the court, the prosecutor appeared to go out of his way to push back against Trump’s attacks. Crabb said the prosecutors who filed the original recommendation that Stone go to prison for between seven and nine years did not defy their superiors or act inappropriately.

“I want to make clear to the court that the confusion was not caused by the original trial team,” he said, adding that it was filed by those prosecutors “in good faith.” Under questioning by Jackson, Crabb confirmed that the original recommendation was approved by a former aide to Barr who was recently installed as U.S. Attorney in Washington, Tim Shea.

Crabb said the confusion stemmed from miscommunication between Barr and Shea, but Crabb declined to elaborate. When the judge asked whether Crabb wrote the revised recommendation, he demurred again, saying that — despite his earlier comments — he was not permitted to discuss “internal deliberations.”

While Trump has denounced the decision to prosecute Stone, Crabb took a contrary position, echoing comments Barr made in an interview last week, where he called the prosecution of Stone “righteous.”

“This is a righteous prosecution and the offenses of conviction are serious,” Crabb said.

It wasn’t the first time last week’s internal DOJ fireworks came up, either.

Just minutes into the hearing, Jackson first alluded to the dramatic events in the case, including Barr’s unusual intervention to reverse the initial sentencing recommendation, which led the four trial prosecutors to withdraw from the case and one of them to quit the department altogether.

Without mentioning any names, the judge suggested that some critics of the original recommendation seemed unusually moved by Stone’s plight, even though the guidelines that DOJ followed — first adopted in the 1980s to rein in judges’ discretion — sometimes produce extraordinarily long sentences.

“For those of you new to this and who woke up last week to the fact that the...guidelines are harsh, I can assure you that defense attorneys and many judges have been making that point for a long time, but we don’t usually succeed in getting the government to agree,” Jackson scoffed.

Later, Jackson noted that the government’s decision to argue that Stone should get less prison time than federal sentencing guidelines recommend was a definite deviation from standard practices adopted by the Trump administration.

“It’s not just a question of good faith, but whether it was fully consistent with current DOJ policy,” she said. “The current policy of this Department of Justice is to charge and prosecute the most serious offense available in order to get the highest guideline level.”

Crabb acknowledged that is “generally” DOJ’s current policy and that line prosecutors are not permitted to deviate from it without approval from higher-ups.

And while Trump has suggested the judge has been cruel towards his allies like former Trump campaign chairman Paul Manafort, Crabb came to the judge’s defense Thursday, saying “the government has the utmost confidence” in her, and praising her “thoughtful analysis and fair sentences” in related cases.

Jackson also declared to the courtroom that Stone’s crimes were not without impact. She said that his obstruction stymied the GOP-led House Intelligence Committee's probe into Russian election interference, which concluded in a highly-criticized April 2018 report that there was no evidence of collusion between Trump’s campaign and Moscow.

“It led to an inaccurate, incomplete and incorrect report,” Jackson said.

The judge also weighed Stone's social media campaign to challenge his prosecution, a controversial put on the court to ensure the judge and staff weren’t facing actual threats of violence.

"This is intolerable to the administration of justice and the courts should not sit idly by, shrug its shoulders and just say it's 'Roger being Roger,’” Jackson said.

Stone, 67, has sought to avoid any prison time. During Thursday’s hearings, his defense argued he had no criminal record and should get a reprieve because he’s a family man about to become a great-grandfather.

“Consider the full scope of the person who stands before you in sentencing," said Seth Ginsberg, a new defense lawyer brought on for sentencing.

“Mr. Stone has many admirable qualities,” Ginsberg added, urging Jackson to look beyond the "larger than life persona" Stone plays on TV. He noted Stone's charity work to help veterans, animal welfare and NFL players suffering from traumatic brain injuries.

Despite Stone’s typical passion for or the spotlight, Ginsberg said the high-profile trial and its attendant publicity had taken a toll on the defendant and his family.

“The process really to some extent has already been the punishment,” Ginsberg insisted.

But Jackson in her closing statement unloaded on how Stone’s defense team for acting so dismissive of the charges during the trial.

"The truth still exists,” she said. “The truth still matters.”

Stone won’t have to start serving his sentence right away. He’s seeking a new trial on the grounds that one of the jurors had a preconceived bias — a decision that Jackson is expected to address in the coming weeks.

Even with the delay, Stone’s fate appears like it now rests with Trump saving an ally with whom he shares a four-decade relationship.

Trump has been arguing in recent weeks that Stone’s crimes were harmless.

“Nobody even knows what he did,” the president said, while inaccurately alleging that the prosecution was based on “a tweet.”

Still, the president has been coy about any plans to offer clemency to Stone, even implausibly claiming to reporters on Tuesday: “I haven’t given it any thought.”

However, Trump did send another clear signal this week of his willingness to exercise his clemency power, by issuing a string of 11 pardons and commutations to other convicted criminals, including high-profile figures like the former Democratic governor of Illinois, Rod Blagojevich, and junk-bond king Michael Milken.

“It's not a question of if," a former senior administration official who remains in close touch with the president and senior aides said when asked about the prospect of a Stone pardon. "It's when."

By law, Stone faced a maximum possible term of 50 years in prison: five years on each of the false-statement counts, five years for obstruction of Congress and as much as 20 years for witness tampering.

However, judges typically sentence in accordance with complex federal sentencing guidelines that tend to call for punishment far less than the maximum for first-time offenders and in many white-collar cases.

The severity of the initial sentencing recommendation stemmed largely from prosecutors’ treatment of several statements by Stone as genuine threats of violence or, at a minimum, having the potential to encourage others to act out. At issue were barbs Stone unleashed at a longtime associate, Randy Credico, as he was mulling how to respond to congressional and Justice Department investigators probing Russian interference in the 2016 election.

“Prepare to die cocksucker,” Stone wrote to Credico in one colorful message. Another seemed to threaten Credico’s beloved therapy animal, promising to “take that dog away from you.”

Credico warned Stone at the time that he had “crossed a red line” by threatening the dog, but at Stone’s trial Credico said he considered Stone a “dog person” and did not think Stone was serious. Credico also sent Jackson a letter last month urging her not to send Stone to jail. The comedian and talk show host said he did not think Stone posed a “direct physical threat,” although Credico did say at the trial that he feared that Stone’s outlandish invective could prompt others to violence.

The prosecutors who handled Stone’s case at trial said the comments were serious enough to trigger an enhancement that added about four to five years to Stone’s recommended sentence. However, the revised proposal Barr submitted said that while the add-on for threats of violence was “perhaps technically applicable,” it would result in a sentence that was “unduly high,” given the facts of Stone’s case.

Stone’s sentence is one of the most serious handed out in a case connected to the Mueller probe.

Manafort got seven-and-a-half years total after a jury convicted him of financial fraud and then he later pleaded guilty to separate charges related to witness tampering and his lobbying work. Rick Gates, a former Trump campaign deputy chairman, is serving 45 days of jail over a series of weekends after pleading guilty to a similar suite of crimes as Manafort. Former Trump attorney Michael Cohen is also serving a three-year prison sentence after pleading guilty to tax fraud and false-statement charges.