"[Stone] remains a convicted felon, and rightly so," Mueller wrote in a Washington Post op-ed.
Stone, a Republican operative and confidant of Trump, was convicted in November of 2019 by a jury in Washington, D.C., on all counts including lying to Congress in connection with its separate investigation into Russian interference, witness tampering and obstructing an official proceeding.
Trump commuted Stone's prison sentence on Friday, less than a week before Stone was about to report to serve time.
Throughout the op-ed, Mueller sought to establish the integrity of the investigation, which Trump and his allies have called a "political witch hunt."
“The work of the special counsel’s office — its report, indictments, guilty pleas and convictions — should speak for itself,” Mueller wrote, breaking a long-held silence since the investigation was completed.
“The women and men who conducted these investigations and prosecutions acted with the highest integrity,” Mueller wrote. “Claims to the contrary are false.”
Mueller said he felt “compelled to respond both to broad claims that our investigation was illegitimate and our motives were improper, and to specific claims that Roger Stone was a victim of our office. Stone was prosecuted and convicted because he committed federal crimes. ”
In a state announcing the commutation Friday, White House press secretary Kayleigh McEnany said that the Republican operative was charged with “alleged crimes” that resulted “solely” from Mueller’s “improper” investigation.
"Roger Stone has already suffered greatly. He was treated very unfairly, as were many others in this case. Roger Stone is now a free man," McEnany said.
The Russia investigation, which Trump has routinely called a “hoax,” did not conclude that Trump's campaign colluded with Russia to interfere in the 2016 election, but detailed a series of contacts and found the campaign welcomed Russia's efforts. Stone was the last of six Trump associates to be charged in connection with Mueller’s investigation.
"Russia’s actions were a threat to America’s democracy. It was critical that they be investigated and understood," Mueller said.
The former FBI director wrote that the investigation “identified numerous links between the Russian government and Trump campaign personnel — Stone among them.”
He described Stone as "central figure" in the investigation because of his communications with Russian intelligence officials, whom the investigation determined were actively seeking to influence the 2016 election through WikiLeaks.
The Mueller investigation found Stone was allegedly aware that WikiLeaks was planning to release emails from former secretary of State Hillary Clinton’s campaign and the Democratic National Committee, viewing the leaks as beneficial to the Trump campaign.