U.S. District Judge Amy Berman Jackson. Photo by Diego M. Radzinschi/THE NATIONAL LAW JOURNAL

When U.S. District Judge Amy Berman Jackson entered her courtroom Thursday to sentence Roger Stone, she was greeted by a Justice Department prosecutor who had not said a word in the trial of President Donald Trump's longtime friend and confidant.

Hanging over the morning's hearing was the tumult of the previous week, a stretch that saw Justice Department leaders intervene in Stone's case to suggest a more lenient sentence than the more than seven-year prison term career prosecutors originally recommended. The extraordinary move—coming just hours after Trump tweeted his objections to the original recommendation—undercut the career prosecutors, prompting all four of them to withdraw from the Stone's case and one to resign from the Justice Department entirely.

So on Thursday, Jackson was met with the prosecutor who stepped in to fill the void: John Crabb, the acting chief leading the criminal division of the U.S. Attorney's Office in Washington. After calling him up speak, Jackson was unsparing as she delved into the remarkable developments in Stone's case.

"I fear that you know less about the case than just about everybody else in the courtroom," she said, pointing to a recently hired defense lawyer for Stone as a possible exception.

Crabb immediately apologized, telling Jackson he wanted "to make clear to the court that this confusion was not made by the original trial team." The team, he said, had been authorized to suggest a sentence of between seven and nine years in prison, adding that the recommendation was made in "good faith."

Crabb's explanation effectively reiterated what senior Justice Department officials said last week: There was a "miscommunication" between the attorney general and U.S. attorney over the sentencing recommendation.

When Jackson pressed for details, asking whether he had been directed to write the second sentencing recommendation, Crabb demurred, saying he was "not at liberty" to discuss internal deliberations.

But he did seek to downplay allegations of political interference in the handling of Stone's case.

"The Department of Justice and the U.S. Attorney's Office is committed to enforcing the law without fear, or favor, or political interference," Crabb said.

Jackson noted the original sentencing recommendation was not withdrawn, and that both memos from the government were signed by the newly appointed acting U.S. attorney in Washington, Timothy Shea.

Jackson appeared vexed by the varying sentencing recommendations, asking Crabb to explain how she should consider the dueling suggestions. And while the initial sentencing recommendation set in motion the dramatic events ahead of the hearing, Jackson emphasized she was never going to impose a sentence of between seven and nine years, saying such a prison term would be "greater than necessary."

Entering Thursday's proceedings, it was an open question whether—or how deeply— Jackson would seek to dive into the Justice Department's maneuvering ahead of the hearing. The intervention in Stone's case drew widespread condemnation and invited suspicions of political interference in the criminal prosecution. More than 2,000 former Justice Department lawyers signed a letter assailing the "interference in the fair administration of justice" and commending the four career prosecutors for standing up for the Justice Department's independence.

Crabb on Thursday defended those original prosecutors in his remarks to Jackson. "This prosecution was and this prosecution is righteous," he said, an apparent rebuke to criticism made by some, including Trump, of the motivations of the original trial team.

Trump, who repeatedly railed against the special counsel investigation into his campaign's ties to Russia, has questioned the motivation behind Stone's prosecution. The president has seized on the participation of two prosecutors on Special Counsel Robert Mueller III's team—Aaron Zelinsky and Adam Jed—and also trained his Twitter ire on Jackson as she has presided over several cases stemming from the Russia investigation.

Without naming Trump, Jackson spoke out against the president's public commentary on Stone's case, labeling it "entirely inappropriate" and declaring that "the court cannot be influenced by those comments."

"The system, for good reasons, demands the responsibility falls to" a neutral party, Jackson said of sentencing. "Not someone who has a long-standing friendship with the defendant, not someone whose political career was helped by the defendant. And certainly not someone" involved in the underlying facts of the case.

Jackson sentenced Stone to 40 months in prison for lying to the House Intelligence Committee as part of its Russia probe, impeding its investigation and witness tampering. But, following a string of pardons and commutations earlier this week, there is widespread speculation that Trump might soon pardon his longtime friend.

In extended, animated remarks leading up to her announcement of Stone's sentence, Jackson said Stone's penalty should transcend politics. His crimes, she said, cut to the core of the Constitution and the institutions it created, including Congress and the judiciary.

She noted that Stone's lying to Congress took place while the federal government was under Republican control, undermining his and others' claims that the longtime GOP operative was a political target.

And in doing so, she echoed a line delivered by one of the original Stone prosecutors, Michael Marando, as he told Stone's jury during closing arguments in November that the "truth still matters."

"The truth still exists," Jackson said Thursday. "The truth still matters."

Read more:

'Flagrant Disregard for the Institutions of Government': Stone Sentenced to Over 3 Years

'A Loss to the Pursuit of Justice': Praise for Roger Stone Prosecutor Who Resigned

The Hardest Thing About Being a Judge? What Courts Say About Sentencing.

Roger Stone's Lawyers Were in Court Today. It Didn't Go Well