Then-FBI Director Robert S. Mueller III attends a Justice Department farewell gathering for him in 2013. (Saul Loeb/AFP/Getty Images)
Tim Weiner's reporting and writing on national security have won the Pulitzer Prize and the National Book Award. He is the author of “Enemies: A History of the FBI” and “Legacy of Ashes: The History of the CIA.”

The week after the 2016 presidential election, I flew to Mexico to talk to Robert S. Mueller III.

The invitation to interview him about national security before an international conference audience came on short notice. The setting was a gilded hall of the palatial National Museum of Art in the historic heart of Mexico City. Mueller was dressed, as always, as if it were 1956, Eisenhower in the White House, Sinatra on the radio. He was relaxed, courtly, charming.

I was reeling over the reality that Donald Trump was going to be president — and the slowly dawning realization that the Russians had wanted him in the White House. I hoped that Mueller, three years out of office as FBI director, might have some thoughts on this politically charged counterintelligence case. Six months to the day after we met, he was appointed special counsel.

If you’re looking for killer quotes, abandon hope. The conference organizers wanted the onstage colloquy to be off the record. But then Mueller and I talked face to face for about an hour offstage, first on a bus and then in a hotel. He responded to an email shortly afterward, via an aide, saying that although he didn’t want to be quoted, save for one sentence, I could recount the day as I saw it.

Given that he has been dead quiet since May 17, 2017, when he became the special counsel, and that he probably won’t be scheduling a news conference anytime soon, I thought this might be the moment for that recollection.

We talked about a uniquely American problem: how to run secret agencies in an open society. He wanted the bureau to serve as an intelligence service under law. When Mueller discussed national security, he invoked civil liberties — and the tug-of-war between them — in the same breath. They were opposing forces; we had to have both.

Mueller made a persuasive case that he’s a civil libertarian. No, that’s not a big part of his reputation. Yes, he ran zealous counterterrorism operations after 9/11, some of them overzealous. But underneath that badge, I thought I detected a part of his heart that bleeds.

He wanted his time at the FBI to be judged not only on work to disrupt and deter terrorism, but on protecting the rights of everyone, including enemies of the state. He wasn’t going to be the guy who got a medal hung around his neck in retirement and a speech saying congratulations, you won the war on terrorism, but we lost our civil liberties.

Since that day in the museum, his investigations have reversed the polarity of public perceptions of the FBI, whose agents execute his orders as special counsel. Liberals who loathed the FBI now claim to love it. Conservatives who revered it now revile it. The ACLU holds rallies nationwide to defend Mueller’s work. President Trump attacks it in 142 tweets as a “WITCH HUNT.”

We may want Mueller to be a lock-’em-up law man, not a civil rights advocate. I think he has the temperament to hold these two opposite ideas at once, and to reconcile them. That is justice in his eyes. He’ll throw the book at Trump if the evidence demands it, but that book is going to contain the Constitution, not just the criminal code.

In Mexico City, Mueller hewed closely to passages in a little-noticed, now nearly forgotten 2002 speech he gave at Stanford Law School, after receiving an award named for Jackson Ralston, a prominent graduate and, later in life, chairman of an ACLU chapter in California. In that speech, he made special mention of COINTELPRO, the attack on “leftists” and “radicals” — Mueller’s text put the words in quotation marks — led by J. Edgar Hoover’s FBI from 1956 through 1971. COINTELPRO aimed to destroy the Rev. Martin Luther King Jr., among thousands of other targets. Mueller vowed in that speech to protect “the constitutional rights of all Americans, including those Americans who wish us ill.” He said much the same in the museum in Mexico.

That was not a widely held position in Washington in the wake of 9/11 — an attack that took place one week after he took over the FBI.

He defended and enforced harsh provisions of the USA Patriot Act. The FBI rounded up 1,200 people in eight weeks after 9/11. None was a member of al-Qaeda. The bureau sharply increased the use of informants as agent provocateurs in Islamic communities.

But there’s another side to that story. Mueller’s agents also were among the very first to blow the whistle on the CIA’s secret prisons, to report the torture and abuses Americans carried out at those black sites and in the bleak chambers of Abu Ghraib. In October 2002, FBI agents at Guantanamo Bay in Cuba opened a running file that they later labeled “War Crimes.”

Mueller soon became something of a lonely voice in a wilderness where the alpha wolves were Vice President Richard B. Cheney and his acolyte, President George W. Bush. In 2004, lest we forget, Mueller confronted Bush and Cheney over their warrantless spying on Americans, the enormous National Security Agency eavesdropping effort code-named Stellar Wind. The NSA was sending the FBI raw data gleaned from the program, which amounted to handing over bulging vacuum cleaner bags the size of blimps. Stellar Wind was COINTELPRO cubed.

Mueller — and the acting attorney general of the United States, who happened to be James B. Comey — determined that this was unconstitutional. On March 11, 2004, Bush ignored them and reauthorized the program alone in the White House.

“The WH was trying to do an end run around the law,” read Mueller’s notes from that day. He drafted a letter of resignation by hand at 1:30 a.m. on March 12. “I am forced to withdraw the FBI from participation in the program,” he wrote. “Further, should the President order the continuance of the FBI’s program … I would be constrained to resign as Director of the FBI.” He was going to take much of the command structure of the Justice Department and the bureau with him, including Comey and the current FBI director, Christopher A. Wray. Bush would not pay that price.

One subject Mueller wouldn’t touch in our conversation was the decision by Comey, his successor as FBI director, to take the hood off the 2016 election and tinker with the engine. But the single thing he chose to put on the record was an insistence that “the FBI director must be above politics,” and the clear context of that comment was Comey. These men are allies now. But I saw back then that they weren’t friends, a fact that Comey has since affirmed: “I’ve never been to his house,” he told members of Congress this month. “I don’t know his children’s names.

Comey has capitalized on his fame. I doubt Mueller will. He comes from a culture almost lost to us, a pure product of an America that essentially ceased to exist in the upheavals of 1968 — the world of the liberal Republican, once an endangered species, now nearly extinct, where working for the government was a patriotic public service, where personality is a private matter and where it is possible to be apolitical. I’ve interviewed presidents and secretaries of state and defense — Gerald Ford, Jimmy Carter, George Shultz, James Baker, Robert Gates — who were battered and scarred by politics, a bit embittered even. Mueller was none of that. Not then anyway. He’d had the sang-froid to stare down a president and emerge unscathed. I suspect he’ll do that again in the fullness of time.