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The revelation of an alleged plot to attack the Canada-U.S. train system by a small cell somehow connected to al-Qaeda's presence in Iran has sparked interest in the relationship between the Sunni Muslim terror group and the Shia Muslim Iranian government. There is no doubt that al-Qaeda has a presence in Iran – but how it relates to the Tehran regime has been murky for years.

The relationship between al-Qaeda and the Islamic Republic of Iran has been shrouded in mystery and secrecy for years. Al-Qaeda operatives have transited through Iran regularly before and after Sept. 11, 2001, and some found sanctuary in Iran after fleeing Afghanistan in late 2001, although the circumstances of their status in Iran was always unclear. But the hints of occasional operational co-operation between al-Qaeda and Tehran are mostly outweighed by the very considerable and public evidence of the deep animosity between Sunni-extremist al-Qaeda and Shia-extremist Iran.

Antipathy for each other is at the root of their ideologies and narratives. It has been most visible in their competition for influence in Iraq, and now also in Syria.

The Sept. 11 plot is a good place to start if we wish to understand the mystery. The 9/11 Commission report concluded that there was evidence of contacts between Osama bin Laden and Iran (through its Lebanese Hezbollah ally) dating back to his years in Khartoum in the mid 1990s.

Mr. bin Laden may even have met with the infamous Hezbollah terrorist Imad Mughniyah back then to share terror tricks. Three of the 9/11 hijackers reportedly travelled from Saudi Arabia to Beirut, then on to Iran and into Afghanistan on a flight with an associate of a senior Hezbollah official, according to the commission's report. Khalid Sheikh Mohammad and Ramzi Binalshibh (the two captured al-Qaeda operatives who masterminded the 9/11 attack) confirmed that eight to 10 of the 9/11 hijackers at one time or another between October, 2000, and February, 2001, transited through Iran on their way to or from Afghanistan for training purposes, taking advantage of the Iranian practice of not stamping Saudi Arabian passports.

The bottom line of the 9/11 report is unequivocal, however: It reports that both Mr. Mohammad and Mr. Binalshibh categorically denied any relationship between the hijackers and Hezbollah. On Iran, the commission concludes: "We have found no evidence that Iran or Hezbollah was aware of the planning for what later became the 9/11 attack." So, at most, this was passive assistance, not actual co-plotting.

After the fall of the Taliban in Kabul, some al-Qaeda members, including bin Laden family members, fled to Iran – though most went into Pakistan. Many have since left Iran, including one of Osama bin Laden's wives who ended up with him in his final hideout in Pakistan. This al-Qaeda presence may have been loosely under the supervision of the Iranian regime at times.

On the other side of the ledger, the animosity between Iran and al-Qaeda is public and abundantly clear. For al-Qaeda and ts allies such as the Afghan Taliban, Shiites are not true Muslims and should be treated at best as outcasts if not apostates. Al-Qaeda's first leader in Iraq, Abu Musaib al Zarqawi, was notoriously vicious in his hatred for the Shia. Al-Qaeda in Iraq still regularly targets Shiite innocents. At the same time, however, al-Qaeda operatives regularly cross Iran to travel between Iraq and Pakistan, some probably unknown to Iranian authorities and others probably tolerated with a blind eye.

Now, in Syria, al-Qaeda is backing the Sunni majority in its civil war with the Shia Alawite minority that backs President Bashar al-Assad. This month Ayman Zawahiri, Osama bin Laden's successor, attacked Iran in an audio message for backing Mr. Assad and for allegedly secretly colluding with America against the global jihad movement.

Despite their animosity, al-Qaeda and Iran can probably find places to quietly co-operate – if only passively. America and its allies are on a collision course with Tehran over Iran's nuclear program. From Tehran's perspective, the war has already begun. Iran's nuclear scientists are being assassinated, its nuclear and missile facilities blown up and its computers hacked. As the confrontation worsens, Iran may look for indirect ways to fight back.

Tehran might not know that al-Qaeda figures in Iran were in touch with an alleged cell in Canada at all – or it might allow al-Qaeda greater use of Iranian territory for communicating with a cell in Canada as a simple way to harass Washington and Ottawa without much risk. "Just turn a blind eye" co-operation is very hard to detect by Western intelligence agencies and almost impossible to prove.

In turn, as the United States puts pressure on al-Qaeda's safe haven in Pakistan, Mr. Zawahiri and his terrorists are likely to start looking for alternative sanctuaries. Iran is right next door. In short, al-Qaeda and Iran still hate each other, but they could find common cause to fight America and Canada.

Bruce Riedel, a former CIA officer and presidential advisor on Middle East and South Asia issues, is senior fellow and director of the Brookings Institution Intelligence Project. He is the author of The Search for Al Qaeda (2008) and Deadly Embrace: Pakistan, America and the Future of Global Jihad (2011).