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Muhanad al-Farekh is shown in a handout photo obtained on Sept. 29, 2017. Intercepted communications and fingerprint evidence revealed in court indicate that Mr. al-Farekh willingly joined al-Qaeda in Afghanistan.HANDOUT/Reuters

A University of Manitoba student turned al-Qaeda member was sentenced in New York to 45 years in prison on Tuesday, the only criminal-justice outcome to date from a global manhunt that began in Canada more than a decade ago.

The result means that Muhanad al-Farekh, a 32-year-old U.S. citizen, will be locked in a penitentiary until he is a senior citizen. Two Canadian co-travellers have remained unaccounted for since the trio disappeared into the Pakistan-Afghanistan borderlands in 2007.

The sprawling case was first reported by The Globe and Mail in a 2009 investigation, The Lost Boys of Winnipeg. Over the years, Mr. al-Farekh evolved into a significant al-Qaeda terrorism suspect, to the point that that, according to news reports, he was placed on a target list for a lethal U.S. drone strike in 2013.

However, U.S. officials concluded he should be captured and brought to face justice in the United States − an outcome that happened three years ago. Intercepted communications and fingerprint evidence revealed in court indicate that Mr. al-Farekh willingly joined al-Qaeda in Afghanistan and went on to plot bombings against U.S. soldiers.

Convicted of terrorism-conspiracy offences last year, Mr. al-Farekh was accused of plotting attacks that included a massive 2009 truck bombing against a U.S. military base. Although the bomb misfired, it injured nearby Afghan women, children and soldiers.

“The defendant, who was born in the United States, came from an upper-income family that afforded him the opportunity to attend university in Canada, receive a college degree, and eventually contribute positively to the world,” a sentencing submission from prosecutors reads. It adds that “together with his friends he embraced hatred and violence, and travelled overseas with the goal of murdering U.S. soldiers.”

Evidence revealed that before his capture, Mr. Al-Farekh became increasingly housebound while hiding out in Afghanistan and Pakistan. “Don’t have many storys [sic] to tell other than being locked up in my house for almost 3 months,” he wrote to a friend in 2013. He added that “I really want to travel to Syria,” because in Afghanistan the “Brothers that are working, they are getting killed.”

Before the sentencing, family members of Mr. Al-Farekh wrote to the judge in Brooklyn, pleading for clemency. They described him as a cosmopolitan young man who was born in Houston, raised in Jordan and the United Arab Emirates, and who had family in Canada. As a teenager he is said to have tended lovingly to horses and, once, a hurt bird.

In the mid-2000s, he became more outwardly pious. “While in Manitoba he was active in the Islamic association and got scholarship in recognition of his active social and religious work,” his father wrote to the court.

Prosecutors took a dimmer view of his time at the University of Manitoba, writing that it was there he met his two Canadian co-accused − Maiwand Yar and Ferid Imam. The three are alleged to have become hooked on videos by the radical U.S. preacher Anwar al-Awlaki, a significant al-Qaeda-aligned figure. He released dozens of online videos before being killed in Yemen by a U.S. drone strike in 2011.

Months later, news reports said, Mr. Al-Farekh emerged in the cross hairs of the same sort of strike, but by then public debates about whether U.S.-citizens who were terrorism suspects should be killed by their own government had had a chilling effect. “Because he [Mr. Al-Farekh] was an American citizen, we needed more information,” one former U.S. official told The New York Times in 2015. “Post-Awlaki, there was a lot of nervousness about this.”

It’s not clear what has happened to the two Canadian co-accused. They are still considered fugitives from police in Canada and the United States.

Mr. Al-Farekh had faced a possible life sentence for his crimes, but the judge ruled he was not completely beyond redemption. His lawyers told the court that he “survived torture in a foreign country” before being brought back to the United States, where he is said to have been kept in solitary confinement.

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