In the torturous history of the U.S. government's black sites, the F.B.I. has long been portrayed as acting with a strong moral compass. Its agents, disgusted with the violence they saw at a secret C.I.A. prison in Thailand, walked out, enabling the bureau to later deploy "clean teams" untainted by torture to interrogate the five men accused of conspiring in the attacks of Sept. 11, 2001. But new information that emerged this week in the Sept. 11 case undermines that F.B.I. narrative. The two intelligence agencies secretly arranged for nine F.B.I. agents to temporarily become C.I.A. operatives in the overseas prison network where the spy agency used torture to interrogate its prisoners. The once-secret program came to light in pretrial proceedings in the death penalty case. The proceedings are currently examining whether the accused mastermind of the Sept. 11 plot, Khalid Shaikh Mohammed, and his four co-defendants voluntarily confessed after years in the black site network, where detainees were waterboarded, beaten, deprived of sleep and isolated to train them to comply with their captors' wishes. At issue is whether the military judge will exclude from the eventual trial the testimony of F.B.I. agents who questioned the defendants. Earlier testimony showed the F.B.I. participating remotely in the C.I.A. interrogations through requests sent by cables to the black sites seeking certain information from specific detainees, including Mr. Mohammed after he was waterboarded 183 times to force him to talk.