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CMP Assistant Commissioner James Malizia answers questions at a press conference April 22, 2013 in Toronto. The RCMP arrested two individuals and charged them with conspiring to carry out a terrorist attack against a VIA passenger train.

The RCMP's assertions that the alleged train-attack plotters were directed by al-Qaeda operatives from Iran provide a potentially chilling wrinkle to Canadian and Western counter-terrorism efforts.

Whether Canada was the primary target, or a way to get at Americans was not clear – al-Qaeda's broad anti-Western agenda, which has sometimes named Canada as a target, makes both possible.

Canada's hard line on Iran – it cut diplomatic ties last year – wouldn't normally make this country an obvious target for al-Qaeda, which has never taken its orders from Iran's ayatollahs. The RCMP said it was not a state-sponsored plot.

But the suggestion that al-Qaeda was plotting attacks from Iran – something Tehran has, according to experts, long prohibited – will raise concerns.

Canada has for years been counted as a target for al-Qaeda, according to the Canadian Security Intelligence Service, and the terrorist network's propaganda has periodically named this country, even if the organization has not successfully attacked here. Al-Qaeda's broad agenda against the West places the U.S. as the chief target, but allies are also on the list. A CSIS threat assessment reportedly found Canada named specifically, along with a half-dozen countries, in documents found when Osama bin Laden was killed. Canada's foreign policy, as a stalwart U.S. ally, former Afghanistan combatant, and staunch Israel supporter, only heightens al-Qaeda's antipathy.

But Iran and al-Qaeda are, on one level, adversaries, on either side of the Shia-Sunni divide, and their affiliates have sometimes fought each other, notably in Iraq.

However, experts have noted that Tehran has harboured several al-Qaeda leaders since the 9/11 attacks, at times detaining them but sometimes assisting them – while insisting, as a form of self-protection, that they refrain from plotting attacks from Iranian soil. More recently, however, some have raised fears the two could eventually work more closely to strike common targets.

The RAND Corporation's Seth G. Jones wrote in a 2012 article in Foreign Affairs that's not happening yet, and that "the terrorist organization would almost certainly refuse Iranian direction." But he also noted al-Qaeda, so far fearful of endangering its safe harbour by plotting attacks from Iran, would want permission to do so – and if pushed by something like an attack, Tehran might forge a working link.

Ray Boisvert, a former assistant director of CSIS, said some al-Qaeda operatives might operate across a porous border with Afghanistan. But Iran has let al-Qaeda leaders move more freely in recent years, and has shown signs it is "acquiescing" to its activities: "They're not chasing them down and stopping them."

Canada is certainly on Tehran's adversary list: the Harper government has cited it as a state sponsor of terror and advocated sanctions against Iran's nuclear program. Ottawa cut off diplomatic ties last year, saying Canadian diplomats could become a target.

Investigators, however, have indicated that al-Qaeda guided the plot from Iran, not that Iran directed it. But the link will still trouble counter-terrorism officials.