Technically, a national security court case now taking place in a Toronto is part of a long effort to determine whether Egyptian-born Mohamed Mahjoub represents a threat to Canada.

But the hearing before Federal Court Justice Edmond Blanchard has turned into something else. It’s no longer just about 52-year-old Mahjoub, a man the government wants deported for his alleged terrorist ties.

Instead it has become about the government itself — its rationale for issuing so-called security certificates against alleged terrorists, the quality of the evidence it uses and the amount of care taken by cabinet ministers who ultimately make these decisions.

First, Mahjoub himself. That CSIS would be interested in him is understandable. Before entering Canada as a refugee in 1995, he had managed a farm in Sudan for Osama Bin Laden. That alone would raise reasonable questions.

But the rationale for his 12-year detention (either in prison or through some form of house arrest) under Canada’s far-reaching security-certificate legislation is becoming increasingly murky.

Ottawa insists that any specific evidence against Mahjoub be kept secret. What it has said publicly is that he was second in command of an Egyptian terrorist organization known as the Vanguards of Conquest.

But events of the last few years have called the nature of this organization into question.

At the federal court hearing this week, Egyptian lawyer Magdi Salem testified, from Cairo via satellite, that security forces under former president Hosni Mubarak invented plots by the Vanguards simply as excuses to round up those viewed as enemies of the regime.

Salem, who also heads the Egyptian bar association’s human rights committee, said that’s why Mahjoub was named. And he pointed out that since Mubarak fell, other alleged members of the Vanguards have been quietly released from Egyptian jails.

Indeed, press reports show that one of those released last year was Ahmed Agiza, who up until then had been regarded by CSIS as the Vanguards’ leader.

Those with long memories might recall that in 2001 Swedish police handed over Agiza and another Muslim living in that country to agents of the U.S. Central Intelligence Agency. The CIA then whisked the pair off to Egypt in a private jet for years of imprisonment and torture.

Was Agiza ever a dangerous terrorist? Sweden doesn’t think so now. This summer, it granted him permanent residency status. It has also awarded him $457,000 in compensation.

If the alleged leader of an alleged terror group is deemed harmless enough to live unhindered in Stockholm, why can’t his alleged number two stay in Canada? I expect those are questions Mahjoub’s lawyers might ask.

Certainly, the federal court hearings have not inspired confidence in the government’s security certification process. Publicly released evidence indicates that Canada’s spy agency relied, directly or indirectly, on Mubarak’s secret service for the bulk of its information.

It’s also clear that CSIS knew some or all of this information was derived from torture. When Salem was asked if torture were common under Mubarak, he seemed surprised anyone would ask. Of course, he said. He had been jailed for two years and tortured. Everyone in a political case was tortured.

Did Canada’s government suspect that allegations against Mahjoub were gleaned from torture? In his testimony last week, former public safety minister Stockwell Day weaved and bobbed around that question.

He insisted he was a hands-on minister who looked closely at every security certificate case carefully before signing off. But he said he couldn’t really remember asking for specific evidence of CSIS’ allegations against Mahjoub. Nor could he remember having suspicions over how that evidence was obtained.

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Oddly enough, Egypt’s change of government might mean that Mahjoub could now be deported there without risk of torture. But it seems he’s determined to stay in Canada. We shall see if he eventually succeeds.

Thomas Walkom's column appears Wednesday, Thursday and Saturday.