A career clandestine operations professional, Kappes supervised the extraordinary rendition program, a non-judicial system of rendering persons suspected of terrorism to secret locations where most of them were interrogated.

Kappes joined the Central Intelligence Agency in 1981 and held a variety of operational assignments in Europe and the Middle East and managerial positions at CIA Headquarters.

John E. McLaughlin, the then-Deputy Director of Central Intelligence, announced his departure the same week Kappes quit, thus exacerbating the rumored management problems for Goss.

[8] Instead, Leon Panetta was appointed to the position in February 2009, and Kappes was retained as DDCIA, the latter a condition set by Feinstein in exchange for her support for the former.

[9][10] On November 4, 2009, in a landmark ruling, Italian judge Oscar Magi convicted 22 American CIA operatives of kidnapping Muslim cleric Osama Moustafa Hassan Nasr, known as Abu Omar, from the streets of Milan in 2003.

[11] Per official reports, Kappes was responsible for the alteration of records regarding the death of a detainee at the 'Salt Pit', a secret CIA interrogation operation in Afghanistan.

According to two former officials who read a CIA inspector general's report on the incident, Kappes coached the base chief—whose identity was withheld at the request of the CIA—on how to respond to the agency's investigators.