“Detainee desired to help Al Qaeda ‘do something big against the U.S.,’ ” one of his co-conspirators, Ammar al-Baluchi, told Guantánamo interrogators, the files say. Mr. Paracha discussed obtaining biological or nuclear weapons as well, though he was concerned that detectors at ports “would make it difficult to smuggle radioactive materials into the country,” the file says.

Image Saifullah Paracha is being held in Guantánamo.

Mr. Paracha’s assessment is among more than 700 classified documents that fill in new details of Al Qaeda’s efforts to make 9/11 just the first in a series of attacks to cripple the United States, intentions thwarted as the Central Intelligence Agency captured Mr. Mohammed and other leaders of the terrorist network.

The plots reportedly discussed by Mr. Mohammed and various operatives, none of them acted upon, included plans for a new wave of aircraft attacks on the West Coast, filling an apartment with leaked natural gas and detonating it, blowing up gas stations and even cutting the cables holding up the Brooklyn Bridge.

For the small circle of Qaeda operatives described in the December 2008 assessment of Mr. Paracha, terrorism appears to have been a family affair. There was Mr. Mohammed, the terrorist network’s top plotter, and his nephew, Mr. Baluchi, who was married to another militant, an American-trained neuroscientist, Aafia Siddiqui. And there was Mr. Paracha and his son, Uzair.

The newly revealed assessments, obtained last year by the group WikiLeaks and provided by another source to The Times, have revived the dispute, nearly as old as the prison, over whether mistreatment of some prisoners there and the prison’s operation outside the criminal justice system invalidate the government’s conclusions about the detainees.