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Parliament Hill’s Peace Tower in the background with the statue of Ivstitia (Justice), outside the Supreme Court of Canada.Fred Lum/The Globe and Mail

He set out to toughen criminal law, demonstrate Parliament's supremacy and reduce the role of the Supreme Court in the nation's life. Instead, Stephen Harper left an ironic legal legacy: a stronger rights charter and emboldened judges, with the Supreme Court more front-and-centre than ever.

As Justin Trudeau begins his tenure, he follows a prime minister who was determined to unmake the Canada that Pierre Trudeau helped to create – by challenging the conventional wisdom that the 1982 Charter of Rights and Freedoms, as interpreted today by judges, sets stern boundaries for what government can do. So he made laws that seemed to give little ground to Charter rights, and changed how judicial appointments work as he sought judges considered less inclined to oppose his agenda.

But Mr. Harper lost to the conventional wisdom. Even judges he had appointed struck down laws he had passed, such as those on mandatory jail terms or illegal drugs. "The balance of power shifted in the last decade even further towards judicial authority at the expense of parliamentary authority," Benjamin Perrin, a constitutional specialist who was the lead justice adviser in the Prime Minister's Office in 2012-2013, says in an interview with The Globe conducted by e-mail. "There is now no controversial social issue in which the court will not have a definitive role."

In taking on judges and the rights charter, Mr. Harper bequeathed to the new Justice Minister, Jody Wilson-Raybound, multiple legal challenges in which her department is involved. The result could be a supreme irony: Unless she moves quickly – on refugee health cuts, on mandatory jail sentences that fall most heavily on aboriginal peoples, on a spate of laws that reduce judges' discretion – the Trudeau government will find that its justice-department lawyers are in court defending Harper-era policies whose goal was to remove perceived liberal bias from the justice system.

One unintended consequence of Mr. Harper's approach is that he left behind court precedents that will limit what any government can do. (Especially unintended: Any tough-on-crime government will face these limits.) "What happened was the old physics rule: For every action, there was an opposite reaction," says Rocco Galati, a Toronto lawyer who successfully challenged Mr. Harper's 2013 appointment of a Supreme Court judge.

The Harper approach was to change the law incrementally. Lots of small increments add up to big change. On murder, he took away the "faint-hope clause" that allowed for parole after 15 years instead of 25. Then he permitted the 25-year waiting period for a parole hearing to be added up in cases of multiple murders – 25 years on each murder. And then he promised life in prison with no parole for especially brutal murders.

But court rulings work the same way. Incremental rulings on Charter rights build, one on top of another. And that is what happened on the Charter's Section 7 – the right to life, liberty and security, which Osgoode Hall associate dean Benjamin Berger calls "the heart of the Charter."

One key instance: Seven years ago, the Conservative government tried to shut down Insite, a Vancouver clinic at which illegal drug users could inject heroin in the presence of a nurse. Denying the facility a federal exemption to the country's drug laws would be a simple way to make the clinic illegal. Not so fast, the Supreme Court said unanimously in 2011. Shutting down the clinic would severely harm, perhaps even kill, drug addicts, a vulnerable population, the court said.

The decision in the Insite case has made it difficult for governments at all levels to limit the rights of the vulnerable on social issues. It became the foundation for the Supreme Court's unanimous rulings striking down federal prostitution laws in 2013 (the court said they endangered prostitutes) and the Criminal Code's ban on assisted suicide last year (the court said it harmed those who were deeply suffering). Judges will feel largely bound to uphold the stronger rights of the vulnerable in future cases, leaving less manoeuvring room for government when it writes laws on such divisive issues.

The consequences of this legacy played out last month in a municipal case in which homeless people won the right to sleep in public parks in Abbotsford, B.C. The city would sometimes spread chicken manure to deter the homeless from setting up camp. B.C. Supreme Court Chief Justice Christopher Hinkson, a Harper appointee, ruled for the homeless and against the city. Government should not cause physical or psychological harm to a vulnerable population, he said, citing the Insite ruling.

And Insite is now being cited in a legal challenge to solitary confinement in the federal prisons, filed in British Columbia. If the new Public Safety Minister, Ralph Goodale, and Ms. Wilson-Raybould, are tempted to defend the status quo on solitary confinement, they may find themselves taking a position on basic Charter rights similar to that taken by the previous government.

The Insite ruling was a watershed, according to Mr. Perrin, now a professor at the University of British Columbia's Allard School of Law. He says it led to a series of decisions "that have made it much more difficult for future governments to legislate on controversial social issues."

The Harper legacy is one Ms. Wilson-Raybould and her successors must take notice of. Unless a prime minister is prepared to use the Charter's "notwithstanding clause" allowing government to opt out of a Charter ruling – which even Mr. Harper, believer in parliamentary supremacy, never did – the rights document inspired by Pierre Trudeau will remain a vital touchstone.

"An attempt to operate Parliament, the government, the executive, without serious reflection on … the Charter," Prof. Berger says, "is one that now in contemporary Canada is doomed to fail."

Sean Fine is The Globe and Mail's justice reporter.

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