The court appearance came a day after Stone was hit with seven criminal counts lodged by Mueller as part of his investigation into Russia's meddling in the 2016 election. Stone was charged with five counts of making false statements, one count of obstructing another probe of Russian interference conducted by the House Intelligence Committee, and one count of witness tampering.
Stone was arrested Friday in a predawn raid by FBI agents at his Florida home, which his lawyer decried as a "spectacle" that was "completely unnecessary."
Immediately after the hearing, Stone spoke to Infowars, the pro-Trump conspiracy website led by Alex Jones, in a phone interview apparently conducted from within the courthouse itself.
"I intend to fight for my life," Stone told Jones. "I think I am being persecuted for being a 40-year friend and supporter" of Trump's.
Stone, who prides himself on his sartorial taste, appeared in court in Broward County sporting a dark polo shirt and jeans and wearing handcuffs.
Trump, without mentioning Stone by name, vented rage against the special counsel in a tweet Friday morning after the scheduled start of Stone's court appearance.
"Greatest Witch Hunt in the History of our Country!" Trump said.
The 24-page indictment alleges that Stone had contacted, and had been contacted by, an array of Trump campaign associates about leaking Democratic officials' stolen information on the eve of the 2016 election to sway the contest against Hillary Clinton.
The organization that coordinated the document-dumping campaign is unnamed in the indictment but clearly refers to WikiLeaks and Julian Assange. That whistleblowing site dumped tranches of emails from the Democratic National Committee and Clinton campaign chairman John Podesta that were allegedly hacked by Russian operatives.
Stone has repeatedly denied colluding with Russia. His lawyer, Grant Smith, told NBC News on Friday that if the special counsel had "found any collusion, they would have charged him with it."
Stone's court appearance began as his former associate and ex-Trump campaign chairman Paul Manafort, another target of Mueller's probe, appeared in court in Washington.
Manafort's hearing related to Mueller's allegation that the Republican operative repeatedly lied in breach of his plea deal with the special counsel. Manafort had pleaded guilty to multiple crimes related to his work for pro-Russia politicians in Ukraine.
"This has nothing to do with the president," White House press secretary Sarah Huckabee Sanders said of Stone's indictment. "The president did nothing wrong. There was no collusion on his part."
Trump's counsel, Jay Sekulow, said: "The indictment today does not allege Russian collusion by Roger Stone or anyone else. Rather, the indictment focuses on alleged false statements Mr. Stone made to Congress."
But the special counsel does implicate multiple top-ranking Trump campaign officials in Stone's indictment. CNBC reported Friday that one such person, referred to as a "high-ranking Trump Campaign official" in the indictment, is former White House chief strategist and Trump campaign CEO Steve Bannon.