A few hours later, speaking at a "Hope for Prisoners" graduation ceremony in Las Vegas, Trump talked about the Stone case, saying, "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."
"I'd love to see it happen," he said, going on to suggest the Stone jury foreperson was "totally tainted," calling her an "anti-Trump activist" without providing specific evidence.
But he added, "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. I think that's the best thing to do," apparently suggesting a pardon was still possible, but not mentioning the word "pardon" or making any specific promises.
"At some point I'll make a determination," Trump said, "but Roger Stone and everybody has to be treated fairly. And this has not been a fair process."
Besides the prison term, Stone was sentenced to 24 months probation and fined $20,000. Stone remains free pending a decision on his motion for a new trial.
"He was not prosecuted, as some have complained, for standing up for the president. He was prosecuted for covering up for the president," Judge Amy Berman Jackson said emphatically at his sentencing, flatly rejecting claims by Stone and Trump that the prosecution was politically motivated and unfair. She also called the actions of the Justice Department in the case "unprecedented," referring to the recent political drama over his case.
Stone's fate took on new significance last week when the career prosecutors who handled the case recommended a sentence of seven to nine years for Stone, who was convicted of lying to Congress and witness tampering in November.
After Trump tweeted that recommendation was a "miscarriage of justice," Attorney General William Barr overruled the prosecutors and the Justice Department submitted a new recommendation calling on Jackson to give Stone a much lighter sentence. Shortly after, in an exclusive interview with ABC News Chief Justice Correspondent Pierre Thomas, Barr warned Trump to stop tweeting and commenting on the case, saying he was making it "impossible" to do his job.
Sources have told ABC News that Barr, who has called the Stone prosecution "righteous," is seriously considering resigning.
Stone, 67, was convicted of misleading congressional investigators on several key elements of their probe into Russian meddling in the 2016 election, including communications he had with the Trump campaign about the WikiLeaks dissemination of damaging documents stolen from Democrats.
ABC News had a team of reporters and producers inside and outside the courthouse.
Here is how the story unfolded.
1:05 p.m. Stone departs courthouse smiling but doesn't say anything
In a wild scene, Stone and his entourage depart the courthouse surrounded by shouting supporters and protesters.
Stone is smiling but says nothing before getting into a waiting SUV.
ABC News' Ali Dukakis was in the courtroom during the sentencing and files these notes:
One could see only Stone’s back as he stood silently with several of his lawyers as Jackson delivered her blistering rebuke of Stone and others who have alleged he was charged because of his political activity and support of President Trump.
"Stone was prosecuted for covering up for the president," Jackson said.
When all was said and done, Stone attorney Bruce Rogow put a hand to Stone’s back in what appeared to be a gesture of emotional support that Stone played off as a signal to go back to the defense table.
There were no tears. His wife and daughter looked shell-shocked, devoid of emotion, not yet digesting the weight of the moment.
12:34 p.m. Judge Jackson sentences Roger Stone to 40 months in prison
He was given 24 months probation as well, plus a $20,000 fine.
Before announcing the sentence, Jackson read lengthy prepared remarks -- during which Stone and three of his lawyers stood before her, hands clasped in front, with expressionless faces.
"This prosecution did not arise because Mr. Stone was being pursued by his political enemies," Jackson said, adding that the government's case came about because Stone "injected himself smack in the center of one of the most significant issues of the day."
She walked through the case, beginning with Stone's role as the Trump campaign's "contact point" to WikiLeaks, his contacts with senior aides to then-candidate Trump in the summer of 2016, and his misleading statements about Stone made to the House Intelligence Committee.
The narrative Jackson gave followed the one presented by prosecutors at Stone's trial. She said at one point, "that is why he was indicted -- not because of his political activities."
"The notion that this case rises and falls on whether Russians colluded in the election ... is false," Jackson added.
"This is not mere equivocation, this is not the product of confusion ... the facts show these answers were clearly false," Jackson said of Stone's comments to the House Intelligence Committee.
Ticking through the rest of the counts Stone was found guilty of committing, Jackson continued to read directly from testimony presented at trial -- including from former Trump adviser Steve Bannon and Randy Credico, the witness Stone was accused of threatening.
"This effort to obstruct the investigation was deliberate, planned," Jackson said. "So that's what the defendant did."
Jackson then turned to other circumstances she must take into account -- Roger Stone's record. She noted that even the letters in support of Stone characterized him as a "bare-knuckled brawler" and a "dirty trickster."
"Those were the letters in support, mind you," she said.
Jackson lauded Stone for his support of family members and using his "voice and political acumen" to advocate for various social efforts such as same-sex marriage and Alzheimer awareness.
"It falls to me to sentence him [based on the merits of the case]," Jackson said.
"Nothing about this case was a joke. It wasn't a prank," Jackson said.
"The government's initial memorandum .. was submitted with an even-handed judgment," she said. "But I am concerned that 7-9 years ... would be greater than necessary."
She called the "actions of the Justice Department" in the past week "unprecedented."
Turning her attention to possible sentencing departures, Jackson said he is healthy and cited his extensive travel as evidence that he is not infirm, which appears to undercut some of what Stone's legal team suggested in their sentencing memorandum.
"He wasn't prosecuted for standing up to for the president," Jackson said.
"I cannot and will not sentence him based on the people he supports ... Roger Stone will not be sentenced for his reputation, or his personality, or his work," Jackson said. "The touchstone in this case is the offense."
"This is not campaign hi-jinks ... he lied to Congress," Jackson said.
Jackson took tremendous issue with statements made by Stone's lawyers: "So what?" she said.
"The truth still persists. The truth still matters ... if it goes unpunished ... everyone loses," Jackson said.
So while the defense can ask, who cares? Jackson hit back:
"Congress cared. The Justice Department ... cared. The jury ... cared. The American people cared. I care."
Jackson then went into her guideline calculations.
11:23 a.m. Judge takes break in proceedings; Stone says he won't speak on his own behalf
"At this point, I want to take a short break," Judge Jackson says.
It is not clear whether she will announce the sentence immediately upon reconvening.
After his defense counsel concluded an impassioned plea for a sentence with no incarceration, Roger Stone rises to say he chooses not to speak on his own behalf.
We are now in a 10-15 minute break.
11:16 a.m. Judge demands government explain sentencing recommendation confusion
The new government prosecutor on Stone's case takes to the lectern to "apologize to the court for any confusion" caused by the Justice Department's dual sentencing recommendation memorandums.
"This confusion was not caused by the original trial team," Crabb says. "There was nothing in bad faith about the prosecution team's recommendation."
Jackson interrupts to ask several questions about who ordered the new memorandum, why an additional memorandum was filed, and what caused any discrepancies in the two documents.
Crabb says the first memorandum was approved by the U.S. attorney.
"What I understand is, there was a miscommunication between the U.S. attorney's office and main Justice," Crabb says, referring back to comments Attorney General Barr made in his interview with ABC News.
Seemingly unsatisfied, Jackson asks Crabb to continue.
"This prosecution was - and this prosecution is - righteous," Crabb says. He then urges the court to impose a substantial term of incarceration.
Pressed by Jackson about how the second memorandum was crafted, Crabb says he could not "engage in a discussion about the internal deliberations."
He refuses to say whether he wrote the memorandum - even though he signed it. Asked if he was ordered to write the second memoradum, Crabb again says he would not discuss it.
Seth Ginsberg, defense counsel for Stone, then takes the lectern to make his case for leniency, calling Judge Jackson's attention to Stone's age and family situation: "He just became a grandfather."
"Mr. Stone has many admirable qualities," Ginsberg adds.
11:04 a.m. Judge Jackson blasts Stone over his social media posts, including those about her
Another proposed sentence enhancement, another win for prosecutors.
Judge Jackson blasts Stone for his out-of-court conduct ahead of his trial, specifically social media posts that criticized the court, the judge, and the government prosecutors.
"It's important to note he didn't just fire off a few intemperate emails ... it wasn't accidental," Judge Jackson says. "He knew exactly what he was doing."
"This is intolerable for the administration of justice," Jackson says. "We had to waste considerable amount of time ... to get the defendant to comply with court orders."
"Therefore I'm going to add the two levels and we are now at a Level 27," Jackson concludes.
Judge Jackson then lists a few mitigating factors before turning to the sentencing grid, which dictates which sentence is appropriate after all sentence enhancements and downward departures are considered.
Both parties will now have an opportunity to speak.
10:55 a.m. Judges sides with defense on proposed sentence enhancement for obstructive conduct
On a third proposed sentence enhancement, Judge Jackson sides with defense counsel -- alleviating some pressure on Stone.
"I'm not going to add two more levels for that," Jackson says, after hearing arguments about a proposed enhancement for additional obstructive conduct.
She is now addressing an additional sentence enhancement - specifically related to Stone's controversial social media postings about Judge Jackson herself.
10:43 a.m. Judge appears to side with government on seriousness of Stone's witness tampering
In a blow to Stone, Judge Jackson has twice sided with prosecutors, who have sought to invoke sentence level increases based on a statute accounting for physical threats.
After an exchange about the veracity of prosecutors' claims that Stone did, in fact, threaten his longtime associate, Randy Credico (and Credico's therapy dog, Bianca), Jackson sides with the government.
Justifying her decision to side with prosecutors, she recites several specific quotes -- many of which include expletives -- that reflect Stone's threats against Credico and his dog.
ABC News Chief Justice Correspondent Pierre Thomas points out that Judge Jackson is taking her time, asking both sides to clarify positions taken in their sentencing memorandums.
She is meticulously taking note of arguments made by both parties and asking for explanations where she perceives ambiguity.
10:24 a.m. Stone's defense lawyer pushes back on charge of witness tampering
Judge Jackson, reading from a piece of paper, ticks through the counts Stone was found guilty of at trial. She runs through an explanation of her sentencing process, interrupting herself briefly to ask a member of the audience to remove his or her sunglasses.
"For those who woke up last week and became persuaded that the guidelines are harsh," Jackson says.
A lawyer for Stone, Seth Ginsberg, then rises to make the case that Stone's conduct and words carried little weight, particularly those used in his conviction for witness tampering.
"Even though the words on their face could be read as threatening," Ginsberg says, "it's our position is that the words themselves did not constitute a threat at all."
"Stone is known for using rough, hyperbolic language. Mr. Credico knew that. He knew that it was Stone being Stone. All bark and no bite," Ginsburg continues, referring to Randy Credico, a mercurial radio host, comedian and impressionist who was a key witness in the government’s case against Stone. Stone is accused of threatening him and his dog.
The government maintained that Credico was a conduit between Stone and Julian Assange, the founder of WikiLeaks – the web operation that published thousands of stolen emails as part of an effort to hurt the campaign of President Trump’s 2016 political opponent, Hillary Clinton.
Reminded by Judge Jackson that she has the power to impose a sentence lower than called for in sentencing guidelines, Ginsburg shoots back: "Yes, and I hope you will!"
10:22 a.m. Trump tweets "FAIRNESS?"
As Stone's sentencing gets underway, President Trump compares Stone's treatment to that of former FBI Director James Comey and former FBI Deputy Director Andrew McCabe.
10:12 a.m. Judge Jackson addresses the Justice Department's sentencing recommendations
Judge Jackson addresses the sentencing memorandum controversy in perfunctory terms -- noting the existence of both the case prosecutors' original recommendation and the subsequent Justice Department recommendation of a much shorter sentence. She stops short of editorializing.
"I also received the government's supplemental memorandum," Jackson says. "I note that the initial memorandum has not been withdrawn."
Jackson goes on to explain additional materials filed as part of the case, including the slew of letters written on Stone's behalf by friends and supporters urging the judge to grant him leniency.
10:05 a.m. Court proceedings have begun
Attorneys for each side have introduced themselves.
"We are here this morning for Roger Stone’s sentencing," Judge Jackson says.
8:45 a.m. Stone arrives amid protests outside courthouse
Stone arrives with his wife, lawyers and entourage at the federal courthouse. Known for his sometimes flashy attire, he's wearing a fedora and sunglasses, smiles but says nothing.
Some supporters hold up a large banner that said "#PardonRogerStone."
Other protesters surround him and shout "traitor!" Some had set up an inflatable rat with a face that resembles that of President Trump.
Overnight, despite Barr's warning not to comment on the case, President Trump at about 2 a.m. tweeted a clip of Fox News host Tucker Carlson calling the Stone case a "shocking insult to the American tradition of equal justice." Trump pinned the tweet on his feed.
This report was featured in the Feb. 2 episode of “Start Here,” ABC News’ daily news podcast.
"Start Here" offers a straightforward look at the day's top stories in 20 minutes. Listen for free every weekday on Apple Podcasts, Google Podcasts, Spotify, the ABC News app or wherever you get your podcasts.