The self-proclaimed "dirty trickster" appeared wearing a conservative suit and left the courthouse without speaking to reporters - days after he made the rounds of the Sunday talk shows to fight back on his indictment.
Stone's attorney, Robert Buschel, pleaded not guilty on Stone's behalf to seven charges: obstruction of a congressional inquiry, witness tampering and five counts of making false statements to Congress.
Magistrate Judge Deborah A. Robinson ordered Stone to return to court at 2 p.m. Friday for a status hearing before Judge Amy Berman Jackson, an Obama appointee.
Robinson warned Stone that failing to appear for the hearing would be a separate offense for which he could face jail time, a fine or both.
"Do you understand, sir?" she asked
"Yes, your honor," he said, speaking for the first time.
The atmosphere outside the courthouse was reminiscent of a political rally, with protesters, supporters and members of the media crammed together on the sidewalk.
Supporters wielded signs saying "Free Stone, jail Hillary" and "We stand with Stone" while chanting Stone's name. Protesters retorted with calls to "Lock him up." At least one person was shown on television holding a sign that said "This is a sign."
Someone started blaring the Beatles song "Back in the U.S.S.R." from a stereo when Stone emerged from the courthouse after the proceedings. His decision to exit from a door on the left instead of the right sent the crowd scrambling to catch a glimpse of him.
Surrounded by attorneys and police, Stone shuffled through the crowd and slid into a black SUV without making any remarks. Members of the media and onlookers surrounded his vehicle, some pushing cameras against its dark tinted windows while police forcefully told people to clear the street.
Attorneys with the special counsel's office and the U.S. attorney's office in Washington, D.C., are jointly handling Stone's case, Jeannie Rhee, a lawyer with Mueller's office, said in court Tuesday.
Mueller has accused Stone of lying to the House Intelligence Committee about his interactions regarding WikiLeaks, the organization that released troves of hacked Democratic emails ahead of the 2016 election that U.S. officials later concluded were stolen by Russian military hackers.
Comment: "Concluded" based on no evidence what-so-ever. It was and remains all a big show to take the heat off what those emails describe and to initiate their campaign against the alternative media.
The 66-year-old risks serving anywhere from one to five years in prison if convicted, according to legal experts.
Stone's appearance came just five days after he was arrested in Florida following an FBI raid of his home that was captured by CNN and aired on national television.
After his first court hearing in Florida, Stone paid the $250,000 bail that had been set to remain out of prison. His travel, however, has been restricted to Florida, New York, Virginia and Washington, D.C.
Before Tuesday's proceedings ended, Michael Marando with the U.S. Attorney's Office in D.C. told Robinson the parties have come to the agreement to designate Stone's case as "complex."
The designation means that the case will not be subject to speedy trial deadlines and is an acknowledgement by both sides that it will take longer to go to trial.
"It basically takes the case out from underneath a lot of deadlines that would otherwise be imposed," said Glenn Kirschner, a former federal prosecutor in D.C.
Randy Lancaster-Short was among Stone's supporters who attended Tuesday's hearing. Outside the courthouse, the political director for the BlakPAC, said he's a friend of Stone's and of the conservative author and conspiracy theorist, Jerome Corsi.
"We all worked together to support the candidacy of Donald Trump," he said. "I think this whole process is dangerous to our republic, for people to not accept a person got elected."
Bill Christeson was among the protesters outside the courthouse holding a sign that read "Dirty Traitor."
"It's dirty traitor, not dirty trickster," he said.
Stone is the sixth associate of President Trump to be charged in connection with Mueller's investigation. He has attracted attention as a result of his public statements appearing to forecast WikiLeaks releases before the election. Stone has denied having advanced knowledge of the hacked emails.
Stone is accused of lying about his interactions with Trump campaign officials and others regarding WikiLeaks in closed-door testimony before the House Intelligence Committee. In one bombshell passage, the indictment alleges that an unidentified senior Trump campaign official was "directed" to contact Stone about future WikiLeaks releases after the group leaked hacked Democratic National Committee emails.
Stone is also alleged to have tried to prevent two associates, Corsi and radio host Randy Credico, from contradicting his false statements to the committee. Both have signaled willingness to testify against him in court.
Stone's indictment does not allege any conspiracy involving the Trump campaign, WikiLeaks or the Russian government. Mueller has not yet charged any Americans in connection with a conspiracy to interfere in the election and is expected to lay out his findings in a report at the conclusion of the investigation.
There is broad speculation that Mueller's probe is in its final stages. Acting Attorney General Matt Whitaker said Monday he believed the investigation to be "close" to completion.
It is possible that Mueller will eventually look to hand Stone's case off to the U.S. attorney's office in Washington.
Stone went on an unusual media tour after his arrest, appearing on major networks including ABC and Fox. People indicted on criminal charges mostly try to stay out of the public eye outside of official court proceedings, but Stone's vocal crusade to prove his innocence has catapulted his case into the national spotlight.
On ABC's "This Week" with George Stephanopoulos, Stone said on Sunday that he thinks he was treated extraordinarily poorly and that the American people need to hear about it.
Stone said he is not a gun owner, has no prior criminal record and that his passport has expired.
"The idea that a 29-member SWAT team in full tactical gear with assault weapons would surround my house, 17 vehicles in my front yard, including two armored vehicles, a helicopter overhead ... and that I would open the door looking down the barrel of assault weapons, that I would be frog-marched out front barefooted, handcuffed when they simply could have contacted me," he said.
Stone has not categorically ruled out striking a deal to cooperate with the investigation, but the prospect appears unlikely at this point. He told Stephanopoulos he expects to be acquitted and vindicated, saying his attorneys believe this indictment is "thin as piss on a rock."
This whole Russian collusion thing has never been about seeking justice, or uncovering the truth. It's been about harassing someone that had the audacity to snatch victory from the darling of the deep state. When Mueller gets done hanging Trump-connected people out to dry for lying, will they double back, and charge Hillary, and a large list of Obama officials on perjury charges? (John Brennan comes to mind) ... Don't hold your breath.