In 2004, then-FBI director Robert S. Mueller III famously threatened to resign from his post if President George W. Bush reauthorized a warrantless wiretapping program that Justice Department lawyers had deemed unconstitutional. After a dramatic confrontation at the foot of the attorney general’s hospital bed, Bush acquiesced, and the program was modified.

The episode — held up as a testament to Mueller’s integrity and independence — was recounted widely after Mueller on Wednesday was tapped to oversee the probe into possible coordination between President Trump’s associates and Russian officials.

But it wasn’t the only time during his 12-year tenure as FBI director that Mueller threatened to leave office in protest. A second, less publicized showdown with the White House came two years later. It wasn’t as clear cut as the confrontation over warrantless wiretapping, but it was every bit as tense.

Under Mueller, who led the FBI from 2001 to 2013, the agency was conducting a corruption investigation of William Jefferson, a Democratic representative from Louisiana. Jefferson was suspected of having accepted hundreds of thousands of dollars in bribes in exchange for promoting a range of business ventures in Africa.

In May 2006, the FBI obtained a warrant to search Jefferson’s congressional office in Washington, as The Washington Post reported at the time.

It was an extraordinary move, the first time in U.S. history that the FBI had conducted a physical search of a congressman’s office. But it was necessary, the FBI argued, because other options had fallen short.

The May 20 raid on Jefferson’s office, which involved 15 FBI agents and lasted 18 hours, set off a firestorm on Capitol Hill. Congressional leaders from both parties accused the FBI of violating the separation of powers. They demanded that the seized documents be returned immediately. White House officials also objected, among them Vice President Richard B. Cheney’s chief of staff, as The Post reported.

During a heated back-and-forth, White House aides ordered the FBI to give the materials back to Jefferson.

Mueller, along with then-Attorney General Alberto Gonzales and his deputy, threatened to resign in protest, as The Post reported. The search was legal, they said, backed by a search warrant signed by a federal judge.

The FBI also alleged that Jefferson was trying to conceal evidence. During a previous search of Jefferson’s house in New Orleans, the congressman was seen stuffing documents into a blue bag in his living room, according to an affidavit justifying the raid on his office. On top of that, the affidavit said, a search of Jefferson’s Washington apartment had uncovered $90,000 in cash hidden in a freezer.

The two sides deadlocked. In the meantime, members of the House called a hearing in which constitutional scholars blasted the raid. One of them, Bruce Fein, testified that the FBI had run afoul of the Constitution’s prohibitions on questioning members of Congress for “Speech or Debate in either House.”

“Let them resign,” Fein said of Mueller and the others. “I am astonished that the president would not have fired them for undertaking this action without consulting him in advance.”

Ultimately, the White House backed down. As a compromise, Jefferson’s documents were placed under seal for 45 days. Some of the materials would remain there much longer, tied up in litigation. In 2009, Jefferson was convicted of nearly a dozen corruption charges and sentenced to 13 years in prison. He is scheduled for release in 2023.

Mueller did not comment publicly on the Jefferson raid, as Barton Gellman wrote in a 2011 Time magazine profile of Mueller. When asked at the time about what principle was at stake, Mueller hesitated:

“I think you’ve perhaps hit on a —” Mueller says, then stops. “I’m just going to stay away from it. I was close, but I’ve just got to stay away from it.”

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