Prosecutors sought a life sentence. But Judge Marcia Cooke balked, noting that there were no specific, identifiable victims of his crimes and that the F.B.I. had known what he was doing for years before arresting him — a fact that she said “does not support the government’s argument that Mr. Hassoun poses such a threat to the community that he needs to be imprisoned for the rest of his life.”

In the lawsuit, Mr. Hassoun’s lawyers accused the government of seeking “to impose what amounts to a life sentence on the very same basis that the trial judge considered and rejected.”

The Departments of Homeland Security and Justice declined to comment.

Complicating matters, the lawsuit says that the F.B.I. has produced a memorandum assessing Mr. Hassoun as a security risk for reasons that go beyond his actions two decades ago, citing allegations that he used unspecified “incendiary rhetoric” in Muslim prayer services at the immigration facility and tried to recruit three unidentified fellow detainees for illegal activities.

Neither the government nor his defense team would provide the memo to The New York Times or describe the purported illegal activities. Ms. Hallett and Mr. Manes called the claims false, and said making the details of such “slander” public would only smear their client’s reputation. Part of their argument is that he has a right to a hearing to confront his accusers and contest the credibility of such claims.

While the dispute over Mr. Hassoun is new, the dilemma it raises is not. A longstanding immigration statute says that when a foreigner is subject to a final removal order, the government should take him into custody for deportation. But it does not dictate what should happen if that goal proves impossible.

In June 2001, the Supreme Court rejected the idea that the government can hold such people indefinitely. Writing for a five-justice majority, Justice Stephen G. Breyer said that it would be unconstitutional to interpret the law as permitting perpetual civil detention, and set a general six-month limit for such custody.

Still, in that case, Zadvydas v. Davis, the majority also suggested that exceptions could be made for “special circumstances,” like if a detainee had a mental illness that caused him to pose a threat to public safety. Justice Breyer also noted that the case before the court in 2001 did not involve terrorism.