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An Amtrak/VIA train from New York to Toronto passes through Oakville April 22, 2013.For the Globe and Mail

At Quebec City's Laval University this spring, Ahmed Abassi was conspicuous by his absence. The science student from Tunisia had missed an important presentation he was to give about nanoparticles.

"He never made it … so I had to give the presentation for him," Bousselham Echchahed, a classmate and fellow researcher, recalled in an interview at a mosque on Thursday. "He left to go back home on his honeymoon in December. I haven't seen him since."

On Thursday, the reason for the young man's disappearance became clear when prosecutors in New York City unsealed a criminal case alleging that Mr. Abassi had been charged with attempting to get false work documents so he could live in the United States and kill Americans. "Ahmed Abassi had an evil purpose for seeking to remain in the United States – to commit acts of terror and develop a network of terrorists here," U.S. Attorney Preet Bharara said in a statement.

Many details about the police case are sketchy. Police say Mr. Abassi entered the United States in March and was immediately placed under FBI surveillance. The charges say he was spotted in New York with a fellow Tunisian science student also residing in Quebec, Chiheb Esseghaier.

On April 22, they were arrested on opposite sides of the border. The RCMP nabbed Mr. Esseghaier in Montreal and accused him of taking part in an "al-Qaeda-supported" plot to derail a passenger train crossing the Canada-U.S. border. The FBI took Mr. Abassi into custody very quietly in New York, grilling him for a week without any scrutiny from media or defence lawyers.

Charges unsealed on Thursday said an undercover FBI officer befriended the two men in New York weeks earlier and taped them as they discussed plans to commit acts of terrorism.

As portrayed by U.S. authorities, Mr. Abassi and Mr. Esseghaier were loose-lipped plotters, more aspirational terrorists than operational ones. Prosecutors say they never took concrete steps toward turning their conspiracies into reality but frequently argued about which kinds of attacks were best.

Mr. Esseghaier, who faces several terrorism charges in Canada, is said by U.S. authorities to have favoured a plot against passenger train. Mr. Abassi allegedly "told the [FBI undercover officer] that while Esseghaier's plans were good, the time was not right," reads a U.S. court document, adding that he "had suggested an alternative plot contaminating the air or water with bacteria in order to kill up to 100,000 people."

U.S. authorities were not able to gather sufficient evidence to charge Mr. Abassi with participating in a terrorist conspiracy. Instead, he is accused of a form of immigration fraud.

Some students at Laval University said Mr. Abassi, who went to Tunsia for his honeymoon this winter, had been having trouble getting a visa to return to Canada. He first arrived in Canada as a student in 2010, not long after Mr. Esseghaier came on similar credentials. Intelligence sources suggest the two men had been monitored ever since they got to Canada.

Police say Mr. Esseghaier took terrorist training overseas and may have had interactions with al-Qaeda members in Iran.

Mr. Abassi has no known history of such travels, but the FBI says he admitted under questioning that he radicalized Mr. Esseghaier years ago.

A New York lawyer acting for Mr. Abassi said the U.S. charges are highly questionable.

"He flatly denies these allegations – he really does," defence attorney Sabrina Shroff said, before adding that her client "is not charged with any terrorism offences. He's charged with visa offences."

In Canada, a second suspect is accused of helping Mr. Esseghaier devise a plot against passenger rail targets. Raed Jaser was also arrested in Toronto on April 22.

The U.S. charges unsealed on Thursday make no mention of Mr. Jaser. The RCMP has never released details about how the railway conspiracy was to have unfolded.

With reports from Joanna Slater in New York, Jane Taber in Halifax, Kathryn Blaze Carlson, Renata D'Aliesio and May Warren in Toronto.