U.S. Attorney Was Forced Out After Clashes Over How to Handle Russia Inquiry

Career prosecutors at the Justice Department do not believe criminal charges are warranted from an investigation seeking to discredit an earlier F.B.I. inquiry into Russia’s attempt to tilt the 2016 election in President Trump’s favor, according to people familiar with the matter.

It leaves unclear what political appointees at the Justice Department might do, given the breadth of Mr. Trump’s demands that it pursue people he perceives as enemies. Already, the U.S. attorney in the Western District of Virginia overseeing the case, Todd Gilbert, was forced to resign in August because he refused to sideline a high-ranking career prosecutor who found the evidence flimsy, the people familiar with the matter said.

Senior Justice Department officials had ordered Mr. Gilbert to open a grand jury investigation into whether anyone at F.B.I. headquarters during and after the Biden administration had mishandled classified documents related to the Russia investigation that Mr. Trump has long decried as a “witch hunt” against him.

Even as news of Mr. Gilbert’s departure over the summer raised concerns about turmoil inside the Justice Department, the events leading up to it have remained unclear until now. The new details highlight how Mr. Trump’s push for criminal prosecutions of those he sees as enemies has led to crises inside multiple U.S. attorneys’ offices, in this instance dooming a top prosecutor in the Western District of Virginia, based in Roanoke. Similar disputes consumed Mr. Gilbert’s counterpart in eastern Virginia, Erik S. Siebert, in recent weeks.

Mr. Gilbert was a longtime Republican legislator in Virginia until he was sworn in as the top prosecutor in July. He was quickly ordered to take up a case championed by the F.B.I. director, Kash Patel, and his deputy, Dan Bongino, after they learned that classified documents had been found inside “burn bags” at F.B.I. headquarters.

For decades, classified documents have been retained on computer servers. When printouts are made of sensitive documents, officials often dispose of them by burning the papers as a security measure. Mr. Patel and Mr. Bongino are among the Trump loyalists who have pressed for an investigation to determine whether senior F.B.I. officials at the time had conspired to protect former F.B.I. and C.I.A. officials by hiding or destroying such documents.

There have been a number of unusual facets to the investigation. The Justice Department tends to try to closely control national security-related investigations in a particular office or team. In this instance, however, the department has dedicated multiple U.S. attorneys’ offices to a set of interconnected issues, all centered on an effort to show misconduct in the Russia investigation, which is nearly a decade old.

Federal prosecutors in western Virginia, rather than in Washington, were assigned the document investigation on the legal theory that jurisdiction was there because the F.B.I. has a classified document storage facility in Winchester, which is in that part of the state, according to people familiar with the case.

Since the investigation began, there has been little indication of any grand jury activity, though a host of former F.B.I. officials voluntarily sat for interviews, according to people familiar with the matter.

Witnesses in the case were questioned by a combination of civil lawyers — not criminal prosecutors — from the Western District of Virginia, as well as criminal prosecutors from the neighboring Eastern District of Virginia and F.B.I. agents. To reassure witnesses that they were not targets of the investigation, witnesses were allowed to be interviewed at their lawyers’ offices, rather than at government buildings.

Defense lawyers who have clients caught up in the case have expressed bafflement at what possible crime could have been committed, and one witness approached earlier this year was told the investigation was being conducted at the specific direction of Mr. Patel.

Shortly after Mr. Gilbert took over as U.S. attorney, senior Justice Department officials instructed him to open an investigation into the handling of secret documents related to Russian intelligence reports, these people said.

After reviewing the evidence, Mr. Gilbert told his superiors that he did not believe there was sufficient evidence to justify a grand jury investigation, these people said. Frustrated by that answer, aides to Attorney General Pam Bondi and her deputy, Todd Blanche, blamed a senior career attorney in the office who they believed had swayed Mr. Gilbert: Zachary Lee, a veteran prosecutor with more than two decades of experience involving public corruption and narcotics, among other issues.

Justice Department officials ordered Mr. Gilbert to replace Mr. Lee with Robert Tracci as his deputy, these people said. After Mr. Lee was demoted, senior department officials suspected Mr. Gilbert was still primarily consulting Mr. Lee, whom they came to view as a holdover from the Biden administration, though he had been hired during the George W. Bush administration and promoted during the first Trump administration, these people added. At one point, Mr. Blanche spoke directly to Mr. Gilbert and offered him more resources to pursue the case, according to one person familiar with the events.

Pressed to further sideline or remove Mr. Lee, Mr. Gilbert refused, these people said. Department officials then informed Mr. Gilbert that he would be fired, and he resigned shortly afterward, posting a GIF on social media with a joke from the movie “Anchorman,” in which the lead character exclaims, “Boy, that escalated quickly!”

Mr. Tracci has since stepped in as the acting U.S. attorney. Mr. Lee, who left the office this month, declined to comment. A Justice Department spokesman declined to comment about the case.

The investigation appears to have petered out, at least for the moment. While investigators have interviewed a number of former F.B.I. officials, there has been little observable activity in the case for weeks, and several people familiar with the work described it as essentially over.

In recent weeks, however, Trump appointees have secured critical indictments against some of Mr. Trump’s nemeses, over the objections of career prosecutors. In the Eastern District of Virginia, Mr. Siebert, a Trump appointee, informed Justice Department officials that there was insufficient evidence to bring charges against Letitia James, New York’s attorney general, and the former F.B.I. director James B. Comey.

Career prosecutors viewed a possible mortgage fraud case against Ms. James as fatally flawed and weak; they also considered the investigation into whether Mr. Comey had lied in testifying to Congress in 2020 as unworthy of charges.

Mr. Trump then fired Mr. Siebert, replacing him with a White House lawyer with no experience as a prosecutor, Lindsey Halligan, who quickly won grand jury indictments against both Mr. Comey and Ms. James.

Both defendants deny wrongdoing, and have accused the Trump administration of misusing the criminal justice system to pursue political vendettas.

Other prosecutors have been under pressure to deliver big-name indictments on politically sensitive cases sought by Mr. Trump and his allies. In Baltimore, charges could be filed any day against the president’s former national security adviser, John R. Bolton, in a long-running investigation into whether he mishandled classified information. That same office has also been assigned to investigate Senator Adam B. Schiff, a California Democrat, to determine if he engaged in mortgage fraud.

In Philadelphia, the U.S. attorney is overseeing an investigation into whether intelligence officials lied about an intelligence assessment drafted in the waning days of the Obama administration. That assessment, long criticized by the president’s supporters, determined Russia had sought to interfere in the 2016 election to benefit Mr. Trump.