The story of Double Agent revolves around Sam Fisher's breakdown after the death of his daughter. Faced with this hardship, Sam takes up an assignment to infiltrate an American-based terrorist group known as the JBA.

Much of the game's story is told in past-tense by the means of a phone call taking place between Fisher and Assistant Director Williams, an NSA executive hired to watch over Lambert and Third Echelon in an effort to keep things in line. These conversations play before or after missions, over a rudimentary collection of images and video. These scenes can vary slightly depending on particular actions taken in the game, and occasionally coincide with other pre-rendered cutscenes, several of which are featured in both games.

One ending exists in this version of Double Agent. Although the result of both games is Sam Fisher being on the run from the NSA, leading into Splinter Cell: Conviction, the events immediately prior play out entirely different from each other.