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Michael Wernick, Clerk of the Privy Council prepare to testify before a House of Commons justice committee in Ottawa on March 6, 2019.Blair Gable/The Globe and Mail

Two days after former justice minister Jody Wilson-Raybould resigned from cabinet, Michael Wernick spoke at a public service communications event. The Clerk of the Privy Council discussed the importance of public trust in government and the role of the civil service in maintaining that confidence. “In a world where facts are contested and people are throwing stuff out for their own particular reasons, it is very important that we project cool and professional," not "defensive and argumentative,” he said. “Our tone must be humble and open, not ‘We know what is best.’” Avoid the fray of “partisan politics,” he advised.

One month later, having been caught in that very fray, Mr. Wernick found himself delivering an unexpected document: a letter addressed to Prime Minister Justin Trudeau advising him of his resignation after 38 years in the civil service.

Here was someone smart and savvy enough to rise through 15 layers of bureaucracy, whose career included a remarkable eight-year tenure as deputy minister in one of the most challenging of government departments. In 2016, when he was first appointed Clerk – a post that comes with a desk in cabinet and a direct line to the Prime Minister – he told The Globe and Mail he’d already been around long enough to “have very thick skin.” He’d assisted in the transition of three governments, both Liberal and Conservative. He was familiar with the frenetic air that settles over Ottawa when a fall election looms – indeed, he cautioned public servants to tread carefully as October approached.

So why, at the end of a decades-long career, is he leaving under a lingering cloud?

The simple answer: Mr. Wernick forgot to take his own advice.

The high-profile drama began with his first appearance before the House of Commons justice committee in February, followed by a second two weeks later. He was called to defend his part in the SNC-Lavalin affair. Mr. Wernick, 61, is among the bureaucrats and political officials who, Ms. Wilson-Raybould alleges, were part of a “consistent and sustained” effort to press her to defer the prosecution of the Quebec engineering and construction giant, now facing criminal charges of bribery and fraud in relation to business dealings in Libya.

His testimony was controversial. Unprompted, he raised the spectre of an assassination attempt during the next election, condemned the “vomitorium” of social media and labelled critical tweets as attempts to intimidate his testimony. On the actual subject at hand, he insisted his actions were consistent with his job. Pressed to more precisely recall a conversation with Ms. Wilson-Raybould, he said, “I was not wearing a wire.” A phone call he took from Kevin Lynch, a former Privy Council Office clerk who is now chair of the SNC-Lavalin board, raised further questions about his role in the file.

Observers decried his demeanour as defensive and hostile, not in keeping with an objective civil servant delivering facts. The Clerk of the Privy Council serves as deputy minister to the prime minister, secretary to cabinet and head of the public service – a tricky balance during the quietest times. But Emmett Macfarlane, an associate professor of political science at the University of Waterloo, said Mr. Wernick invited accusations of partisanship by “looking like he was cheerleading” for the Trudeau government. “We have, under our parliamentary system, an expectation of political neutrality,” Prof. Macfarlane said. “Wernick’s performance at those committees at least gave rise to negative perceptions about that.”

In his “retirement” letter to the Prime Minister, Mr. Wernick acknowledged this perceived conflict: "It is now apparent that there is no path for me to have a relationship of mutual trust and respect with the leaders of the Opposition parties.”

Whether he crossed the line or, as he claims, just did his job, this is not the end anyone anticipated for a man described as the “quintessential public servant.” Mr. Wernick declined repeated requests to be interviewed for this story. But his many speeches as Clerk are posted online as part of his own effort to improve transparency in the office. Read together, his remarks offer a sense of his passionate commitment to a skilled, nimble public service, his view of the clerk’s role as “a soft power” in government and the need to be non-partisan in the midst of an often fraught political system.

By the time Mr. Wernick resigned, he was directly responsible for a staff of 900 and had attended more than 300 cabinet meetings over 10 years. Last November, he told an audience of newly promoted public service executives that what wakes him up at night were not policy decisions, but whether he had placed the right person in the job.

He described his role as secretary to the cabinet as trying to provide ministers “with as much evidence and facts and due diligence as possible.” He liked to use the word “deliverology” to emphasize the need for public servants to “deliver results.” And while he had been given the latitude to have a public presence, he said, in a speech last May, “usually we are not the centre of attention, nor should we be.” He advised adopting a persona that is “relentless, resilient, happy warrior-like.” In one speech, he cautioned: “Poor people skills will end your career.”

Ask people about the highlights of Michael Wernick’s career, and they will, invariably, cite his time as deputy minister of the Indigenous affairs department, a challenging and exhausting post known for a high rate of staff churn. Under Stephen Harper’s Conservative government, Mr. Wernick’s tenure lasted through four cabinet ministers. Chuck Strahl, who was minister from 2007 to 2010, said in an interview this week that Mr. Wernick was a “a steady hand” who “knew how to get things done.” During their time together, for example, they shepherded the Indian Residential Schools apology and passed legislation that created rights for Indigenous women to matrimonial property. He’s “not the guy who told jokes around the table, " Mr. Strahl said. “But I didn’t need warm and gushy to make my day work.”

Once, the former minister recalled yelling at a department committee that was trying to create an optional identity card for Indigenous Canadians. It was a process, to Mr. Strahl’s mind, that was taking too long and cost too much money. “I was probably angrier than I should have been,” he said. “But he smoothed it over." As a deputy minister, he could read the room and adjust. “He didn’t try to push a wet noodle uphill.”

On the other side of the table, Mr. Wernick drew mixed reviews. Phil Fontaine, who served as national chief of the Assembly of First Nations while Mr. Wernick was deputy minister, spoke highly of him, even if the two did not always see eye to eye – such as when the Harper government introduced the First Nations Financial Transparency Act. “He and I had a very solid, productive working relationship,” Mr. Fontaine said in a recent interview.

Some Indigenous groups, however, were less impressed by Mr. Wernick’s management style – in particular, the Algonquins of Barriere Lake, who in June, 2007, set up a campsite on Parliament Hill to protest a lack of progress on land management and social issues such as housing. On the eve of Canada Day, when a prominent protest might have dampened the country’s birthday celebrations, Mr. Wernick visited the protesters and negotiated a deal to appoint a special representative to facilitate talks. It was only a temporary truce.

The next year, in August, several dozen residents of Barriere Lake staged a noisy protest outside the deputy minister’s home on Ottawa’s upscale Clemow Avenue, this time demanding that the government affirm their customary practice of choosing community leaders. (On social media, they even circulated a wanted poster with his face on it.) It was recognition of what they viewed as Mr. Wernick’s negative influence, said Shiri Pasternak, an assistant professor of criminology at Toronto’s Ryerson University who has written a book about the issues facing Barriere Lake. “They had dealt with government for so long, they were wise enough to know who was pulling the strings.”

In March, 2015, he became a controversial player in another protest, while serving on the board of governors for Ottawa’s Carleton University. During a meeting, a small group of students marched in, chanting on megaphones to criticize high tuition fees, and forced an adjournment. Later, an e-mail was leaked in which Mr. Wernick compared the students to “Brownshirts and Maoists” and proposed that they be sanctioned for their actions. “It really reflected that he did not consider protest a part of a robust democracy,” suggested protester Michael Bueckert, then vice-president of the graduate student association.

Mr. Wernick also demonstrated a willingness to step in when a question of fairness was at stake. As Clerk, he prioritized mental health, raising the issue of self-care in speeches and finalizing a new mental-health strategy for the public service. Bill Wilkerson, a workplace consultant who worked on the strategy with staff in Mr. Wernick’s office, recalled an e-mail exchange he had with the Clerk last December. Mr. Wilkerson had been contacted about a young mother with mental-health issues who had been called before a panel to justify missing a few days of language training, a process not in keeping with the new strategy . “I hope you will investigate,” Mr. Wilkerson e-mailed. Not 30 minutes later, Mr. Wernick responded: “I will. M.”

He has a personal connection to the issue: Last year, his son, who worked as a Liberal staffer, publicly disclosed his history of depression and suicide attempts in an effort to galvanize MPs to encourage a healthier work-life balance.

By the time Mr. Wernick sat down before the justice committee, he was not a neophyte in politics or protest – or even negative social-media campaigns. Former colleagues suggest he would have been especially affronted at the suggestion that he, after decades of espousing a non-partisan public service, had personally acted in a partisan manner. And yet, as more than one senior former bureaucrat observed, if he had given his evidence dispassionately and answered the questions in the “humble” and “cool” tone that he himself advised, the events of late might have taken a different turn.

Mr. Strahl said he recalls a different deputy minister once telling him that while the job requires a person to be professional and objective, over time, “just to keep your sanity, you become a part of the government" because you need to believe your work is worthwhile.

Maintaining that balance is tricky with one hat, let alone the Clerk’s three. Prof. Macfarlane said Mr. Wernick’s resignation was the honourable decision, given the importance of the “neutrality of the civil service.” He said the man tapped to replace him – fellow career bureaucrat Ian Shugart, who will officially take over in the coming weeks – will now have to be especially careful to avoid "the trap of becoming an advocate or cheerleader,” even while working so closely with the Prime Minister.

As Mr. Wernick once advised those rising up the ranks: “Suit up and go into the fray, and be as ready as possible.” But also remember: “The tone you set is crucial.”