The federal judge overseeing former President Donald J. Trump’s classified documents case on Saturday rejected an effort by one of his co-defendants to have the charges he is facing dismissed by claiming that he was the victim of a vindictive prosecution by the government.

The co-defendant, Walt Nauta, who works as a personal aide to Mr. Trump, had accused prosecutors in the office of the special counsel, Jack Smith, of unfairly indicting him because he declined to help their efforts to build a case against the former president by testifying against him in front of a grand jury.

Mr. Nauta’s lawyer, Stanley Woodward Jr., also claimed that at a meeting at the Justice Department two years ago, prosecutors had threatened to derail a judgeship he was seeking if he did not prevail on his client to turn on Mr. Trump.

But in an order issued on Saturday night, Judge Aileen M. Cannon rejected those arguments, ruling that even though Mr. Nauta had refused to provide testimony against Mr. Trump, there was “no evidence suggesting that charges were brought to punish him for doing so.”

And while Judge Cannon refused to weigh in on the details about Mr. Woodward’s claims that prosecutors had sought to twist his arm to win Mr. Nauta’s cooperation, she denied his vindictive prosecution motion because, as she noted, he had claimed that the government was biased against him, not against his client, as required by the law.

The indictment in the documents case, which was filed last June in Federal District Court in Fort Pierce, Fla., accuses Mr. Nauta of conspiring with Mr. Trump to hide from the government several boxes of classified materials that the former president removed from the White House when he left office and took to Mar-a-Lago, his private club and residence in Florida.

Prosecutors say that Mr. Nauta, who also worked for Mr. Trump while he was in office, took part in a related plot to destroy security camera footage of Mr. Nauta and another Mar-a-Lago employee, Carlos De Oliveira, moving the boxes. Both men have also been charged with lying to investigators working on the case.

Mr. Woodward’s claim that one of Mr. Smith’s top deputies, Jay I. Bratt, tried to strong-arm him during a meeting at the Justice Department into getting Mr. Nauta to cooperate was a highly personal flashpoint in the case — and one that prosecutors have vehemently rejected.

At a hearing in Fort Pierce in May, Mr. Bratt’s colleague, David Harbach, told Judge Cannon the account was a complete fiction.

“The story about what happened at that meeting is a fantasy,” Mr. Harbach said. “It did not happen.”

In her order, Judge Cannon appeared to seek the middle ground, noting that she did not “infer misconduct on the part of prosecutors or doubt Mr. Woodward’s representations that he has conveyed his recollection honestly.”

She also pointed out that the Justice Department’s own internal watchdog arm, the Office of Professional Responsibility, was looking into Mr. Woodward’s allegations, but was holding any investigation “in abeyance pending completion of this case.”

Mr. Trump has filed his own vindictive prosecution motion against Mr. Smith and his team, accusing them of bringing the charges in the case in a partisan effort to derail his presidential campaign. The motion also accused the government of unfairly targeting Mr. Trump when other public figures who have been found in possession of classified documents — among them President Biden — were never indicted.

Judge Cannon has not yet ruled on Mr. Trump’s motion, but noted in her order on Saturday that her decision to reject Mr. Nauta’s motion “shall not be construed as commenting on the merits” of the former president’s claims.

The judge has slowly been working her way through a barrage of motions to dismiss the charges in the case filed by lawyers for both Mr. Trump and his two co-defendants.

Earlier this week, Mr. Trump’s lawyers asked her for permission to file additional legal briefs on one of those motions, claiming that he enjoyed immunity from prosecution, in the wake of a landmark Supreme Court ruling that granted him wide protection against criminal charges stemming from actions he took in his official role as president.

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