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Hassan Almrei (C) and unidentified interpretor in court July 20, 2005.David Major

Once a member of Canada's so-called "Secret Trial Five," Hassan Almrei took the Canadian government to court. Deemed an al-Qaeda threat after Sept. 11, 2001, and held on a security certificate for almost eight years, he eventually won his struggle against secret accusers and secret evidence.

"I am satisfied that Hassan Almrei has not engaged in terrorism," Federal Court judge Richard Mosley ruled in 2009. Quashing the case against Mr. Almrei, the judge even accused the Canadian Security Intelligence Service of breaching its "duty of candour to the Court" by embellishing its case.

But the story did not end there.

New Federal Court documents obtained by The Globe and Mail show that Mr. Almrei, a 40-year-old from Syria, has returned to court after finding out his application for permanent residency in Canada could be turned down because of allegations from federal authorities that he may be suspected of providing people with false documents.

"My position is it's unfair. It's double jeopardy. It's abuse of process," said lawyer Lorne Waldman, in an interview on Wednesday.

Mr. Waldman added that Justice Mosley will have to rule on the new issues surrounding his client, and whether the government can rely on questionable evidence.

Security certificates were back in the news on Wednesday, when Canada's top court ruled against another one of the group of five, Mohamed Harkat.

In the early 2000s, CSIS accused Mr. Harkat, Mr. Almrei and three others from the Arab world of being al-Qaeda threats, but they went to court and blocked the government's attempts to deport them.

After the favourable 2009 ruling, Mr. Almrei renewed his application for permanent residency. He got refugee status after coming to Canada in 1999, even though he had spent several years in Afghanistan with an Islamist fighting faction during the civil war.

CSIS alleged this was akin to being part of al-Qaeda. Mr. Almrei has always denied it.

In May, 2010, Mr. Almrei sued the federal government alleging negligent investigation and false imprisonment.

In an affidavit related to his immigration application, he says, he says that, two years later, he bought a condo, but he got a letter from his bank, TD Canada Trust, indicating it might cancel his mortgage "to comply with federal regulations and economic sanctions."

That fall, he was summoned to an immigration office in Scarborough for an interview with CSIS officials about his immigration application. Mr. Almrei says he was asked how he felt about the revolt against Bashar al-Assad in his homeland.

Mr. Waldman wrote CSIS to ask why they were back on the case. Federal Court documents show the agency's leaders replied that immigration officials had asked for a background check on Mr. Almrei. "CSIS will process this request as expeditiously as possible," reads a June, 2012, letter from a CSIS deputy director, Andy Ellis.

The next year, as Mr. Almrei was preparing to go to court to speed things up, he got a letter from Canada's border agency. The Sept. 6, 2013, letter explained that he could be considered inadmissible under a legal clause blocking individuals involved in "people smuggling, trafficking in persons or money laundering."

The allegations, first made in 2001, are that, before his security-certificate ordeal, Mr. Almrei got a false Canadian passport for a traveller from Afghanistan who also became an al-Qaeda suspect after Sept. 11.

No federal agency has found Mr. Almrei inadmissible yet. The process is halted while he argues in Federal Court that this is a rehash of the security-certificate case.

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