In early 2002, as the Bush administration hunted for Osama bin Laden, pressed its war in Afghanistan and set its sights on Saddam Hussein’s Iraq, John Bolton saw another looming threat: that Cuba was secretly developing biological weapons.

Bolton, who was then the State Department’s undersecretary for arms control issues, included a warning about the Cuban threat in a draft of a speech and sent it around the department for the necessary clearance. A biological warfare analyst wrote back that Bolton’s proposed comments overstated what U.S. intelligence agencies really knew about the matter, and, as routinely happens, suggested some small changes.

The analyst was summoned to Bolton’s office. “He got very red in the face, and shaking his finger at me, and explained to me that I was acting way beyond my position,” the analyst, Christian Westermann, recalled later during a Senate inquiry. Bolton then demanded that Westermann’s supervisor remove him permanently from the biological weapons portfolio, thundering that “he wasn’t going to be told what he could say by a mid-level munchkin.”

Last week, President Donald Trump named Bolton to be his new national security adviser, a job that would arguably make him the government’s most important arbiter of competing views on foreign policy and a key judge of what intelligence information reaches the president on the most serious threats to national security.

The nomination — which does not require Senate confirmation — has drawn attention mainly for Bolton’s combative bureaucratic style and the hawkish views he has espoused in three Republican administrations and as a Fox News analyst. Among other ideas, Bolton has advocated overthrowing the Islamic government of Iran, bombing that country’s nuclear facilities, and (just last month) taking preemptive military action against North Korea.

But many foreign policy experts, including some who worked closely with him, argue that the more significant issue for Bolton’s new role may be his history as a consumer of intelligence that does not conform to his views, and the lengths to which he has sometimes gone to try to suppress analyses that he sees as wrong or misinformed.

An examination of Bolton’s record, based on interviews with some of his former colleagues and the Senate hearings on his nomination in 2005 to be the U.S. ambassador to the United Nations, reveal a tendency to aggressively embrace intelligence that supported his positions, while discounting information that undercut those views. The confrontations that arose from that approach have often been ascribed to partisanship or sharp elbows, but even some conservative veterans of the Bush administration accused Bolton of exaggerating, minimizing or cherry-picking intelligence information to bolster his policy positions, and of retaliating to try to silence intelligence professionals with whom he disagreed.

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“Anyone who is so cavalier not just with intelligence, but with facts, and so ideologically driven, is unfit to be national security adviser,” said Robert Hutchings, who dealt extensively with Bolton as head of the National Intelligence Council, a high-level agency that synthesizes analysis from across the intelligence community to produce strategic assessments for policymakers. “He’s impervious to information that goes against his preconceived ideological views.”

Bolton declined to comment for this article, but he has dismissed such allegations in the past. During the contentious hearings on his nomination as Washington’s U.N. envoy in 2005, he told the Senate Foreign Relations Committee that his disputes with analysts were based on legitimate questions about the quality of information they produced, and what Bolton asserted were the analysts’ failures to adhere to proper procedures, rather than his ideological views.

“When you lose trust and confidence in somebody in a professional environment, it’s a problem, especially when it’s in the intelligence area,” Bolton testified. “I didn’t seek to have these people fired, I didn’t seek to have discipline imposed on them, I said, ‘I’ve lost trust in them, and are there other portfolios they could follow.’”

Bolton’s allies acknowledge that his bellicose personality can rub people the wrong way. But they said he is often more thoughtful and disciplined in private than in public, and they praised his formidable bureaucratic skills as essential to the White House post.

“You cannot say he is not an able government actor,” said Stewart Baker, who was general counsel of the Bush National Security Agency and of a commission that reviewed intelligence issues relating to the Iraq War. “He knows how government works and knows how to make it work toward new goals. Part of the problem he has faced is just how sharp he is at debate, at finding problems and articulating them in short, pithy phrases and delivering a message the foreign policy establishment doesn’t like.”

Since the creation of the National Security Council in 1947, the role of the national security adviser has reflected the differing power centers and policy views of successive administrations. The job consists of two sets of duties, said Richard Haass, a former head of policy planning for the State Department. The first is to identify issues requiring the council’s attention, assemble intelligence and analysis, lay out policy options and move the government’s security apparatus to necessary decisions. The second role is to serve as a private adviser to the president, one who presents a range of views from across the government, and counsel on the best course. “The trick is not to let your personal preference and advocacy get in your way,” said Haass, who is now the president of the Council on Foreign Relations. “Not a lot of people can do that.”

Haass, who worked under Brent Scowcroft on the National Security Council staff of George H.W. Bush during the first Gulf War, cited Scowcroft as “the gold standard” for skill, discipline and restraint in the job. “He was scrupulous in being an honest broker,” said Haass. “So much so that people in the Cabinet were willing to let him convey their positions to the president.”

Although Haass described Bolton as an intelligent and forceful advocate, he said there are questions about his judgment and temperament, especially since he will be counseling a president with no previous government or foreign policy experience.

Baker, the former NSA lawyer, predicted Bolton will be effective at pushing the ensemble of government agencies to implement policy decisions. “I expect him to be quite good at that,” Baker said. “He has a good understanding of government behavior. And he’s smart and tough and committed to effective action.”

Bolton’s approach has generated scrutiny over the years. After he was nominated for the United Nations job in March of 2005, the Senate Foreign Relations Committee interviewed 35 witnesses and reviewed 800 pages of documents and communications from the State Department, the CIA and the Agency for International Development. In examining Bolton’s tenure as the department’s undersecretary for arms control and international security, skeptical Democrats noted that he had been a vocal proponent of invading Iraq in 2003 — and of the faulty intelligence that the Bush administration produced about Iraqi weapons of mass destruction.

Among the more stinging voices raised against Bolton was that of Hutchings, a veteran diplomat who headed the National Intelligence Council from 2003 to 2005. Hutchings told the Senate committee that the intelligence community had raised strong objections to congressional testimony that Bolton was preparing in the summer of 2003 about the U.S. assessment of Syria’s nascent nuclear program. The intelligence community thought Bolton exaggerated the threat of Syrian weapons development, according to Hutchings and Senate documents.

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Bolton took “isolated facts and made much more of them to build a case than I thought the intelligence warranted,” Hutchings said, according to the Senate committee report. “It was, sort of, cherry-picking of little factoids, and little isolated bits were drawn out to present the starkest possible case.”

In response, Bolton described the conflict that arose over the Syria issue as part of the standard back-and-forth between intelligence agencies and policymakers. Interviewed this week, Hutchings, now a professor of national security studies at the University of Texas’ Lyndon B. Johnson School of Public Affairs, said his opinion about Bolton has not changed. He called Trump’s choice of Bolton “dangerous, not just unfortunate,” and warned that it would increase the risk of an ill-advised war with North Korea and other adversaries.

The 2005 Senate inquiry also delved into complaints that Bolton pressured and mistreated subordinates who differed with him on various intelligence and policy issues. Officials testified that Bolton tried to block the promotion of a young official in in the State Department’s non-proliferation bureau who had received glowing reviews from his superiors. The official, Rexon Ryu, was said to have played a role in removing some of the most controversial allegations about Iraq’s weapons programs from a much-criticized speech that Secretary of State Colin Powell gave at the U.N. Security Council on the eve of the war.

Bolton’s clash with the biological weapons analyst Westermann in 2002 became State Department lore. The argument had its origins in Bolton’s view that the U.S. intelligence community had gravely underestimated the Cuban threat, in part because of the influence of a senior Pentagon intelligence analyst, Ana Belen Montes, who was arrested in 2001 on charges of spying for Cuba.

The speech that Bolton submitted for State Department clearance in February of 2002 warned of the potential “dual use” of Cuba’s advanced biotechnology industry, according to testimony and interviews. Bolton wanted to assert that the U.S. believed Fidel Castro’s government “has a developmental offensive biological warfare program and is providing assistance to other rogue state programs,” according to the Senate report.

That language triggered an objection from Westermann, a decorated Navy combat veteran and former arms inspector who handled the chemical and biological weapons account in the State Department’s Bureau of Intelligence and Research. After Westermann raised his concern, the passage was toned down to say that the U.S. “believes that Cuba has at least a limited offensive biological warfare research and development effort. Cuba has provided dual-use biotechnology to other rogue states. We’re concerned that such technology could support BW programs in those states.”

After dressing down Westermann, Bolton pressed Westermann’s supervisor to remove him from his subject matter portfolio — a move that officials described as tantamount to dismissal.

“People stay on their accounts a long time,” a former State Department intelligence colleague of Westermann said in an interview. “If you remove him from the account, that means he basically loses his job. Bolton went out of his way to bully him. It was beyond the pale.”

Other, more senior State Department officials described Bolton’s behavior as unprecedented. “Asking me to fire an intelligence analyst is a singular event in my career,” former Assistant Secretary Carl Ford, who oversaw the intelligence bureau at the time, said in an interview. “Threatening to have someone fired for not altering intelligence judgments to suit them, that is uniquely Bolton. I have worked in both intelligence and policy positions. Even the most opinionated people with reputations of being difficult never even suggested they were thinking about doing something so outrageous.”

Bolton and his defenders said he was angry because the analyst had communicated with others about the matter without telling him. They pointed out that Westermann kept his job in the end. Nonetheless, news of the harangue spread like wildfire in a culture that prides itself on encouraging analysts to provide rigorous, unvarnished assessments to policymakers, regardless of their power or politics.

Secretary of State Powell, who was known to criticize Bolton privately, later visited the intelligence bureau to show support for Westermann and the other analysts, according to interviews and testimony. Westermann’s star rose further after it became known that he had been a rare voice of skepticism about allegations that Iraq had weapons of mass destruction.

The Cuba dossier triggered another clash only months after the Westermann incident. This time, Bolton’s target was a senior CIA analyst, Fulton Armstrong, who was serving as the intelligence community’s National Intelligence Officer for Latin America. Although Armstrong focused on the Havana regime’s political motivations, he and other CIA officers also challenged Bolton’s public statements about possible Cuban efforts to develop biological weapons.

“We all agreed that what Bolton wanted to say was exaggerating to the point of cooking the intelligence,” Armstrong recalled in an interview. “No one ever stated that Bolton did not have the right to put out any judgment he wanted. Our position was you can say whatever you want, but don’t use us to validate it.”

Bolton and one of his bureaucratic allies Otto Reich, then the assistant secretary for Western Hemisphere Affairs, assailed Armstrong, according to testimony and interviews. In July 2002, Bolton drove out to the CIA’s Virginia headquarters and demanded that a senior official remove Armstrong from his post.

This time, it was the agency’s deputy director, John McLaughlin, who told Bolton, “No.”

“It’s perfectly all right for a policymaker to express disagreement,” McLaughlin said during the later Senate inquiry. “But I think it’s different to then request, because of the disagreement, that the person be transferred. And — unless there is malfeasance involved here — and, in this case, I had high regard for the individual’s work; therefore, I had a strong negative reaction to the suggestion about moving him.”

Bolton said he had “one conversation” at the CIA about Armstrong, then did not revisit the issue. But interviews and the Senate report indicate that the campaign against the Latin America specialist lasted months, if not years. One senator described it as “a vendetta.” Armstrong said the retaliation also had a wider, chilling effect, because the national intelligence officer speaks for the combined work of 15 agencies.

As for Bolton himself, the Republican-dominated committee voted 10-8 in favor of his nomination. Sen. Richard Lugar, R-Ind., the committee chairman, said the cases cited by Bolton’s opponents were overstated. Whatever disputes may have arisen, Bolton “always accepted the final judgment of the intelligence community,” Lugar said. In the face of heated opposition to the nomination in the full Senate, President Bush gave Bolton a recess appointment.

Bolton and other Bush administration policy officials continued to insist on the validity of their view that Cuba was pursuing a bioweapon research and development program. However, by 2005, the U.S. intelligence community concluded that “it is unclear whether Cuba has an active offensive biological warfare effort now, or even had one in the past.”

By 2010, under the Obama administration, an annual State Department report on the issue dropped any references to a bioweapons threat from Cuba. The “available information did not indicate,” the report said, that Cuba was involved in any weapons activities prohibited by international agreement.