In the campaign against al-Qaeda, several senior leaders in the organization were captured by the CIA in 2002. They were subjected to what has been described as torture or enhanced interrogation techniques, according to the U.S. government. The interrogations of two of the key leaders were videotaped.

In 2005, while head of the Clandestine Service, Rodriguez ordered that videotape recordings of two 2002 CIA interrogations be destroyed. CIA officials initially stated that the recordings were destroyed to protect the identity of the interrogators, after they were no longer of intelligence value to any investigations. “He would always say, ‘I‘m not going to let my people get nailed for something they were ordered to do,’” said Robert Richer, Rodriguez’s deputy recalling conversations with his boss about the tapes. It was later revealed that the deputy to Kyle “Dusty” Foggo, then executive director of the CIA, wrote in an e-mail that Rodriguez thought “the heat from destroying is nothing compared with what it would be if the tapes ever got into public domain—he said that out of context they would make us look terrible; it would be ‘devastating’ to us.”