The public statement from the former special counsel known for remaining silent was a signal of just how far Trump, Attorney General William Barr and Trump's Republican allies in Congress have sought to attack and undermine the two-year investigation into Russian election interference.
In recent months, Barr has pushed to lighten Stone's now-commuted sentence and is attempting to drop Flynn's lying charge, while the Trump administration has declassified a series of documents that Republicans and the Trump campaign have used to attack the origins of the Russia probe -- and Trump's 2020 presumptive opponent, former Vice President Joe Biden.
Mueller's op-ed directly rebutted the White House's announcement that Trump would commute Stone's sentence. The White House had called Mueller's work a "baseless investigation" and "witch hunt," and Stone's prosecution "the product of recklessness borne of frustration and malice" from "overzealous prosecutors."
Mueller wrote that the prosecutors acted "with the highest integrity. Claims to the contrary are false." He reiterated that Stone was rightly convicted of obstruction, lying to Congress and witness tampering, and that Russian efforts to interfere with the election to help the Trump campaign deserved investigation.
A representative for Mueller declined to comment.
During the two-year investigation, Mueller's team was notorious for its silence, speaking only through its final report and court filings against multiple members of Trump's team, including Stone and Flynn. But in recent months as the attacks on the investigation have amplified, members of the special counsel team have begun to get more vocal, especially about Stone, who still insists he was unfairly convicted.
But Mueller's decision to publish an op-ed was a step even further.
Several people familiar with Mueller have emphasized the former FBI director's long-time unwillingness to break ranks from the Justice Department and his strict approach to stay out of the political arena.
But Barr has dulled nearly every publicly known prosecution Mueller left for the department to finish and launched his own review of the FBI's work on the probe, while Trump has continuously attacked the investigation as an illegitimate one, claiming it tried to undermine his election win.
Mueller's investigation did not establish a criminal conspiracy between Trump's campaign and Russia. But he uncovered evidence that people inside and associated with the Trump campaign welcomed and encouraged Russian activity that they thought could help their candidate win.
He also documented extensive contacts between Russians and Trump campaign officials and multiple attempts by Trump to obstruct the Russia investigation.
Prosecutors follow Mueller's lead
Until recently, the prosecutors who worked in the special counsel's office stayed in line with the silence of a boss they revere. Many had their own reasons for not speaking, according to half a dozen Washington, DC, lawyers familiar with their thinking. A few still work for the Justice Department, but many left the special counsel's office for lucrative private law firm positions.
Some, until recent weeks, believed stepping up to defend their work wouldn't make a difference in the public discourse because the public had access to the 448-page report. Some took consolation in their belief that the Mueller report would stand up to scrutiny over time and the investigation ultimately will be on the right side of history.
A few cautiously tested the waters -- yet still refused to speak about the Mueller investigation itself.
Andrew Goldstein, for instance, who worked on both the Russia and the Trump obstruction investigations for Mueller, signed his name to a list of ex-Southern District of New York prosecutors condemning Barr's removal of that office's head Geoffrey Berman. "The actions of the President and the Attorney General are an attack on the concept that investigations should be conducted in a nonpartisan manner," their open letter said.
In late June, Zelinsky, a Baltimore-based prosecutor still employed by DOJ, testified about Barr's politicization of the department in its handling Stone's sentencing.
"I have been told by the Department of Justice that my testimony today should adhere to the four corners of the Special Counsel's Office report," Zelinsky told to House Judiciary Committee. Speaking about the Stone case after Mueller closed his office, "I was told there was heavy political pressure from the highest levels of the Department of Justice to cut Roger Stone a break."
After Stone's commutation Friday, Zelinsky released a statement through his lawyer that said he "stands by his testimony and the findings of Special Counsel Mueller's investigation."
Before Zelinsky's testimony, Democrats on Capitol Hill initially reached out to another Stone prosecutor, Jonathan Kravis, gauging his willingness to testify.
"I am convinced that the department's conduct in the Stone and Flynn cases will do lasting damage to the institution," Kravis wrote in the Post.
Testimony could be on the horizon
Now Mueller himself could be asked to return to Capitol Hill to testify, following his stilted appearance last year before the House Judiciary and Intelligence Committees.
Senate Judiciary Chairman Lindsey Graham on Saturday said he would call Mueller in to testify.
Graham is leading one of two Republican Senate committee investigations into the origins of the Mueller investigation and the FBI's Russia probe that's accelerating a years-long effort among Republicans in Congress to cast doubt on the validity of the special counsel's work.
Democrats on the Senate Judiciary Committee have said they also want to hear from Mueller. At a committee meeting last month where Graham received broad subpoena authorization for his probe, Democrats said the committee should be calling Mueller to testify. "I think this side would very well like to have him here," said Sen. Dianne Feinstein of California, the top Democrat on the panel.
Graham said he agreed -- though he suggested someone like Weissmann might be better to testify.
If a hearing does happen, Democrats on the committee would want to hear from Mueller's top deputies and the prosecutors on the Stone and Flynn cases in addition to Mueller himself, according to a source familiar with the matter.