In the FBI Prouty was a special agent on an international terrorism squad. She worked on the USS Cole bombing case, the Khobar Towers bombing case, the Laurence Foley case, and other terrorism cases. In about 2003 she joined the CIA. She thought the CIA would allow her cultural background and linguistic abilities to be used more effectively in her work. She felt that in the FBI, linguists were treated as "second class citizens".