This article was produced in partnership with the Pulitzer Center on Crisis Reporting.

GUANTÁNAMO BAY, Cuba — By the time the C.I.A. delivered Khalid Shaikh Mohammed to the military prison at Guantánamo Bay in 2006, it had already extracted confessions from him through interrogations that included waterboarding, rectal abuse, sleep deprivation and other forms of torture.

But none of what Mr. Mohammed said during his three and a half years in secret C.I.A. prisons could be used in the military commission trial he would face on charges that he was the architect of the Sept. 11, 2001, terrorist attacks. So within months of his arrival at Guantánamo Bay, the Bush administration had F.B.I. agents question him and other Qaeda suspects to obtain fresh, ostensibly lawful confessions. Prosecutors called the new interrogators “clean teams.”

Now defense lawyers in the Sept. 11 case — which has been stuck in pretrial hearings since 2012 and will not go to trial before next year — are stepping up their arguments that those teams were not so clean after all.

They say that they have growing evidence that the F.B.I. played some role in the interrogations during the years when the suspects were in the secret prisons by feeding questions to the C.I.A., and that the C.I.A. kept a hand in the case after the prisoners were sent to Guantánamo. The result, they contend, is a blurring of lines that undercuts the assertion that the confessions extracted after torture could be legally separated from those given by Mr. Mohammed and his four alleged accomplices to the F.B.I. at Guantánamo.