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Prosecutor Saritha Komatireddy, left, points at Muhanad al Farekh, right, in a court sketch of a trial in which Mr. Farekh stands accused of federal terrorism charges in New York.Jane Rosenberg

In a quiet courtroom, Ahmad Yar described his shock and disbelief when his younger brother vanished just months before finishing university.

First, the family received a vague and troubling letter from his brother, Maiwand, Mr. Yar recalled, then a voice-mail message at their home in Calgary from a number in Pakistan. "I am where I want to be," his brother said.

Alarmed, Mr. Yar travelled across the world to try to find his brother. In the northwestern city of Peshawar, he located a hotel where Maiwand and two friends, all fellow students at the University of Manitoba, had stayed for three days. Then their trail went cold.

Read more: Family fears U.S. has killed Winnipeg's 'lost boys' of jihad

The trio – dubbed the "Lost Boys" of Winnipeg – travelled to the tribal areas of Pakistan to join al-Qaeda, prosecutors say, in a case that prompted concern at the highest levels of the U.S. and Canadian governments. Now, details of their mysterious disappearance that have never been made public are being released as part of a trial under way in New York.

At the federal courthouse in Brooklyn, one member of the Winnipeg trio, Muhanad al-Farekh, is facing federal terrorism charges after being captured in Pakistan in 2014.

The trial is shedding light on some of the enduring questions in the case, including how three university students allegedly became enthralled by jihadi ideology and decided to leave behind their lives in Canada.

Their disappearance in 2007 would prove a harbinger of things to come: In the years that followed, more than 100 young Canadians sought to join radical militant groups such as the Islamic State.

Mr. Farekh, who is a U.S. citizen, has pleaded not guilty to the charges, which carry a maximum sentence of life in prison. The witnesses for the prosecution have included current and former U.S. military personnel, forensic experts and a graduate of the University of Manitoba who was friends with Mr. Farekh, Maiwand Yar and Ferid Imam, the trio that disappeared. An Air Canada executive corroborated the flights they took to leave the country on March 6, 2007, sitting next to each other as they flew from Winnipeg to Karachi.

The picture that has emerged so far is of three students with a deepening attachment to the teachings of Anwar al Awlaki, a radical American cleric who was targeted and killed in 2011 by a U.S. drone strike in Yemen because the government considered him a highly dangerous member of al-Qaeda.

One witness testified that the three friends, then in their 20s, discussed with excitement a lecture by Mr. Awlaki about jihad. Mr. Imam and Mr. Yar, both Canadian citizens, exchanged e-mails on where to find the cleric's sermons online.

Prosecutors also showed jurors a brief clip from early 2007 in which Mr. Farekh sits at a computer in Winnipeg and urges Mr. Yar to watch a YouTube video created by a Sunni militant group in Iraq (at the time, the insurgency in Iraq was at its height). "This is it! This is a very good one, come look at this," Mr. Farekh says with enthusiasm. He is wearing a white T-shirt bearing the name of a Canadian fitness association.

The story of the missing men first became public in a 2010 investigation by The Globe and Mail, which revealed their alleged path from a Canadian university campus to al-Qaeda membership in Pakistan.

The fates of Mr. Imam and Mr. Yar remain unknown, although they have never returned to either Canada or the United States.

In the coming days, prosecutors plan to call several people previously convicted of terrorism offences as witnesses in the case, who will testify that they crossed paths with Mr. Farekh and Mr. Imam in al-Qaeda camps in Pakistan. They include Najibullah Zazi and Zarein Ahmedzay, two U.S. citizens who pleaded guilty to a plot to carry out suicide bombings in the New York subway. David Ruhnke, one of Mr. Farekh's lawyers, warned jurors not to trust such testimony. "This case is built in part on witnesses who have committed terrible crimes themselves," he said.

Mr. Farekh, 31, was once considered such a threat that U.S. authorities engaged in a debate over whether to kill him in a drone strike, according to a report in The New York Times.

Unlike Mr. Yar and Mr. Imam, who are Canadians, Mr. Farekh was born in Texas and raised in Dubai. His American citizenship led U.S. officials to pursue his capture and later transfer him to face charges in New York.

More than a dozen fingerprints that matched Mr. Farekh were found on sticky brown packing tape inside an unexploded truck bomb outside a U.S. military base in Afghanistan, an FBI expert testified. Mr. Farekh is "an American who sought to kill other Americans," said Saritha Komatireddy, a federal prosecutor, in her opening argument.

One witness for the prosecution was Youcef Soufi, now a professor at the University of British Columbia. Prof. Soufi told jurors that he has a vivid memory of his earliest conversation with Mr. Farekh: It was in a computer lab at the University of Manitoba, where both were students. Mr. Farekh was funny and inquisitive and the two young men eventually became friends.

Last Thursday, they saw each other for the first time since Mr. Farekh disappeared a decade ago. Mr. Farekh, wearing a blue blazer and sitting at a table with his lawyers, watched intently as Prof. Soufi entered the courtroom.

On the witness stand, Prof. Soufi described how he grew closer to Mr. Farekh, Mr. Yar, Mr. Imam and one other University of Manitoba student when the five young men made a pilgrimage together to Saudi Arabia in late 2006.

He also recalled conversations that took on heightened significance after the three men vanished from campus a few months later. Mr. Imam, for instance, had said that he had difficulty empathizing with victims of terrorist attacks. Mr. Yar, meanwhile, had claimed that the actions of jihadi groups such as the Taliban were beyond reproach. "For me, it was a very scary statement," Prof. Soufi said.

Both Mr. Yar and Mr. Imam received military training from al-Qaeda in a remote area of Pakistan near the Afghan border, prosecutors say. Mr. Imam later allegedly became a weapons trainer for the group.

Two years after leaving Canada, Mr. Yar sent his family a nine-page handwritten letter in which he writes that members of al-Qaeda and the Taliban are "the best people in the world" who want only "to apply the rulings of Allah." He knows this from direct experience, he writes, because he has spent time with them.

After receiving the letter in early 2009, Ahmad Yar, Maiwand's eldest brother, said he immediately contacted the Canadian Security Intelligence Service. In the letter, Maiwand asks for the contact details of relatives in Pakistan, which the family provided via e-mail (the Yar family is originally from Afghanistan).

About a week later, a relative helped arrange a phone call with Maiwand.

On the call, his family told him, "We are still missing you … we still love you," the elder Mr. Yar recalled. They agreed to speak again in a week. When the family called the number in Pakistan they had been given, this time an unfamiliar voice answered, speaking in Pashto. "He says, 'Your brother has died,' " Mr. Yar said. The family has heard nothing from Maiwand since.

With a report from Colin Freeze in Toronto

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