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Jane Philpott listens to an address at the B.C. Assembly of First Nations annual general meeting at the Musqueam First Nation, in Vancouver on Thursday, Sept. 19, 2019. Ms. Philpott’s story should stand out as a remarkable tale from 2019.

DARRYL DYCK/The Canadian Press

Justin Trudeau was damaged by the SNC-Lavalin affair but limped back to power with a minority government. The former attorney-general who accused him of political intrusions in a criminal prosecution, Jody Wilson-Raybould, now sits across the aisle as an independent; she was named Newsmaker of 2019 by The Canadian Press wire service.

But one figure from the affair didn’t return to Ottawa: Jane Philpott.

The former senior cabinet minister wasn’t really one of the chief actors in the scandal. She didn’t have any role in the SNC-Lavalin Group Inc. prosecution. She did a rare thing: She resigned from cabinet because she felt the government wasn’t being honest.

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She didn’t quit politics, or her party. Mr. Trudeau threw her out of the Liberal caucus, along with Ms. Wilson-Raybould. When she ran for re-election as an independent in her riding of Markham-Stouffville, she lost to Liberal MP Helena Jaczek.

MPs, including good ones, lose in every election. But Ms. Philpott’s story should stand out as a remarkable tale from 2019. She did what many Canadians want politicians to do. And she was turfed out of politics.

Ms. Philpott is an unlikely rebel. Mr. Trudeau argued that she and Ms. Wilson-Raybould had to be expelled from caucus for the sake of party unity. Most of the MPs in the Liberal caucus wanted them expelled, too: In their eyes, they had undermined the Liberal Party from within.

Some Liberal insiders whispered rumours that in the weeks before she resigned, Ms. Philpott had been conspiring to remove Mr. Trudeau and have him replaced temporarily by then-Public Safety Minister Ralph Goodale. CBC journalist Aaron Wherry, in his book Promise and Peril, recounted that cabinet minister Patty Hajdu had warned Mr. Goodale his name was being floated as a possible interim prime minister.

What really happened, according to Ms. Philpott, was not a cabal, but the what-if discussions of a fretting Liberal cabinet. And she wasn’t trying to find a replacement for Mr. Trudeau: “Absolutely not,” she said.

“I wasn’t personally working toward that,” Ms. Philpott said in an interview at a coffee shop in Stouffville, Ont., in November, after her election loss. “There were other cabinet ministers who were also greatly shaken by what took place, and there were conversations around, ‘Oh my gosh, where is this going to go?' ”

At the time, Ms. Philpott clearly didn’t know, either. Although she still hasn’t recounted many of the details of what happened, citing cabinet confidentiality, she has said she advised Mr. Trudeau to acknowledge a mistake, apologize and move on.

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Cabinet ministers are expected to speak with one voice, and the SNC-Lavalin affair was so high profile she couldn’t avoid questions about it. So she quit cabinet to sit as a Liberal backbencher. She gave an interview in which she told a journalist there was “much more to the story.”

There was. And in retrospect, Ms. Philpott’s actual criticisms were restrained. Other Liberals, such as Toronto MP Nathaniel Erskine-Smith, have said the Prime Minister’s Office collectively crossed a line. Ms. Philpott’s offence was taking a high-profile action that showed she felt a principle was at stake.

She did not want to repeat Mr. Trudeau’s wholesale denials of pressure on the attorney-general – the PM called the allegations false. Ministers were given similar lines. “Those allegations were not false,” she said. “And I’m not going to go out there and say that they were false. I draw the line at lying.

“And I think that I could have continued as a caucus member if they hadn’t been so annoyed at me.”

That hope was long past when she spoke, still wistfully, in November, in a break from packing up three offices and her Ottawa apartment. She was feeling regret for her constituency staff, who has built up expertise and relationships that would suddenly stop.

A medical doctor, she worked for the better part of a decade in Niger. In Canada, she started the Give a Day to AIDS campaign, encouraging people to give a day’s pay. When Paul Martin appeared at a fundraiser, she told him her frustrations at inequities; he spoke to her about politics. When she was elected as an MP in 2015, she told The Globe and Mail she saw politics as “medicine writ large.”

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Inside government, she was seen as one of Mr. Trudeau’s most effective ministers. At her first cabinet meeting, then as Health Minister, she was made chair of the task force charged with bringing in 25,000 Syrian refugees. She is proudest of some of things most people never saw, such as approving the use of prescription-grade heroin in addiction clinics over the political concerns of political operatives. Her medical background, she said, allowed her to explain: “You don’t need to be afraid. We’re actually saving people’s lives. We’re making the streets safer.”

For a month after resigning, Ms. Philpott did remain in the Liberal caucus. There were discussions, notably between Mr. Trudeau’s team and Ms. Wilson-Raybould, about what would happen next. But Ms. Philpott said that from the time she resigned from cabinet on March 4 to the day the PM called her in to say she would be expelled from the Liberal caucus on April 2, Mr. Trudeau never spoke to her personally.

Looking back, Ms. Philpott still questioned why she wasn’t able to stay in the Liberal caucus as a backbencher when other Liberals such as Mr. Erskine-Smith were allowed to disagree. Is it because he is a man? Ms. Philpott shrugged, inconclusive. “There are lots of men that have been able to say contrary things,” she said. “Women are expected to follow.”

Her campaign as an independent brought in hundreds of volunteers, many previous backers of other parties. She said she thought she had a shot. But on the doorsteps, voters expressed a desire to choose a prime minister, or vote against the party leader they dislike, but especially, a concern that if they vote for an independent MP, the riding will somehow miss out on the spoils of party politics.

“We would hear over and over again, ‘We love you, Jane, we think you’re fantastic, but we’re really worried about what an independent can do.’ ”

Ms. Philpott’s remarkable resignation has faded from view. But it is a tale of how Canadian politics works. She made a point of principle. When that clashed with the leader, there was no room for her in the party.

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“The voters say that’s okay. Essentially,” she said. “Or there is something more important than that. To me, that is disappointing.

“I’m sure most people in the voting booth weren’t saying to themselves, ‘We don’t mind if the Prime Minister kicks out caucus members.’ But to a certain extent the effect is the same.”

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