Mr. Trump is correct that nothing produced publicly by Mr. Mueller to date has claimed any wrongdoing by the president nor any illegal collaboration with the Russians seeking to influence the 2016 election. The indictment of the Russians — who are accused of flooding Facebook and other social media with disinformation and propaganda — cited only contact with “unwitting individuals” connected with Mr. Trump’s campaign.
The charges against Mr. Manafort and Mr. Gates depict an expansive money-laundering and fraud operation stemming from their work for Ukrainian leaders aligned with Moscow, not from their involvement in the campaign. Michael T. Flynn, the president’s former national security adviser, and George Papadopoulos, a former campaign adviser, pleaded guilty to lying to the F.B.I. about their contacts with Russians or intermediaries but not to criminal acts related to collusion.
John M. Dowd, the president’s private lawyer, pointed to Mr. Trump’s cooperation with the investigation as evidence that he had nothing to hide. He noted that the White House had voluntarily turned over more than 20,000 pages to Mr. Mueller, including documents related to Mr. Flynn and Mr. Comey, and the campaign provided 1.4 million pages.
More than 20 White House officials, including eight members of the counsel’s office, voluntarily gave interviews to the special counsel or congressional investigators, as did 17 campaign employees and 11 others affiliated with the campaign, he added.
“I give great credit to the president for his extraordinary cooperation with the special counsel,” Mr. Dowd said.
Still, as the pileup at the courthouse indicates, allies of Mr. Trump acknowledged that the investigation had taken a toll.
“The good news for the White House is that more than 18 months since the F.B.I. probe began, there is still no evidence of Russian collusion,” said Christopher Ruddy, the chief executive of Newsmax and a friend of Mr. Trump. “The bad news is that the special counsel has a scorched-earth prosecution aimed at crushing the president’s associates.”
“I don’t think the president is worried about the investigation himself,” he added, “but it clearly bothers him that people are being prosecuted simply because they worked for his campaign.”
Inside the White House, officials expressed calm resignation on Friday as Mr. Gates marched into the courthouse. But there was low-grade concern out of recognition that Mr. Gates was in a lot of meetings over a long period of time.
While Mr. Gates joined the campaign with Mr. Manafort, his longtime business partner and mentor, he stayed after Mr. Manafort was fired. He rode on Mr. Trump’s campaign plane and served as liaison to the Republican National Committee. After the election victory, he joined the transition as a right hand to Thomas J. Barrack Jr., the president’s close friend who ran the inaugural operation.
The fact that Mr. Gates was allowed to plead guilty to just two relatively lower-level charges indicated to legal experts that he must have something of value for Mr. Mueller. The presumption in Mr. Trump’s circle is that Mr. Gates may not have any incriminating information about the president but could be a dangerous witness against Mr. Manafort, who in turn could threaten Mr. Trump.
Mr. Manafort participated in a meeting in June 2016 along with Donald Trump Jr., the candidate’s son, and Jared Kushner, his son-in-law, with a Russian lawyer on the promise of receiving incriminating information about Hillary Clinton on behalf of Russia’s government.
Mr. Manafort also reportedly offered during the campaign to give “private briefings” to Oleg V. Deripaska, a Russian oligarch allied with President Vladimir V. Putin who claimed Mr. Manafort owed him $19 million. Prosecutors are interested in learning how a Republican convention platform plank on Russia’s intervention in Ukraine was watered down.
On the other hand, Mr. Trump’s defenders said Mr. Gates’s credibility as a witness may be tainted by the fact that one of the charges he pleaded guilty to was lying to the F.B.I. even as he was negotiating his plea deal. Ty Cobb, the White House special counsel, has said that Mr. Manafort has no damaging information against Mr. Trump. Mr. Manafort insisted again on Friday that he was innocent and would fight the “untrue piled up charges.”
Mr. Trump’s argument that none of this has anything to do with him resonates with many of his supporters, who have echoed his repeated insistence that there was no collusion with Russia. But being surrounded by people who are prosecuted has damaged other presidents even when they were not directly implicated.
Jimmy Carter endured significant political damage when his confidant and budget director, Bert Lance, was accused of banking irregularities. Even putting aside the Iran-contra scandal and the Monica S. Lewinsky affair, Ronald Reagan and Bill Clinton were besieged by investigations of their aides unrelated to them. In Reagan’s era, it became known as the “sleaze factor.” Mr. Clinton’s team drew the scrutiny of six independent counsels other than Kenneth W. Starr.
In the current case, the targets so far have included not just a “coffee boy,” as Mr. Papadopoulos was described by an adviser to Mr. Trump, but the president’s top two campaign officials and national security adviser. While Mr. Trump has dismissed the relevance of allegations against Mr. Manafort because they involved business dealings before the campaign, the latest indictment claims that he was scheming to defraud banks while serving as Mr. Trump’s chairman.
Moreover, it remains unclear why he volunteered to work for Mr. Trump’s campaign without pay at a time when he was experiencing significant financial pressure.
Mr. Trump’s defenders have focused on questioning the original basis for the investigation, accusing the F.B.I. of misconduct in relying on an unverified dossier assembled by a former British spy hired by investigators working for Mrs. Clinton’s campaign.
To the extent that Mr. Mueller is exploring whether Mr. Trump obstructed justice by firing Mr. Comey, the president’s defenders contend that under the Constitution, he has the power to dismiss executive branch officials and dictate their work. They also point to testimony by Mr. Comey and other officials who said the investigation was not impeded.
Therefore, they argue, the original order appointing Mr. Mueller was itself invalid and should be revoked.
In the meantime, they are left to interpret the clues from Mr. Mueller’s actions just like everyone else. David B. Rivkin Jr., a former White House and Justice Department lawyer under Reagan and President George Bush, said the totality of Mr. Mueller’s actions still did not add up to a threat to Mr. Trump.
“It doesn’t make sense to unfold piecemeal an indictment of Russian entities and Russians if you have any hope of building a collusion case. It makes no logical sense,” he said. “To me, at least, what he’s done does underscore that there’s no collusion there. That leaves him with the obstruction of justice narrative which I think is constitutionally flawed and isn’t going to go anywhere.”
Mr. Wittes said Mr. Mueller’s actions could be seen as building a pyramid — establishing that there was a Russian influence campaign and assembling a group of cooperating witnesses. But the special counsel has not tipped his hand yet.
“The basic contours of the puzzle is that he’s constructed his actions in a way that we don’t know where it’s leading,” he said, “and that’s on purpose.”