Call of Juarez: The Cartel revolves around a undercover team that has been put together in order to investigate a bombing of an LAPD office. The events pick up in the meeting room where the team is put together, consisting of Ben McCall, an LAPD detective who’s as close to the Western ideals as the game can get, an FBI agent Kim Evans, and Eddie Guerra from DEA. This undercover team is tasked to work in secrecy and carry out their investigation of the bombing, with possible involvement of the local gangsters as well as the Mendoza cartel from Mexico. By granting freedom to achieve their goals, the team begins by attempting to provoke a gang war by destroying drugs that belong to one gang while impersonating the Cartel.

The player can choose which one of the three characters to control, each having their own choice of weapons and special abilities. Sometimes enemies will be laying down suppressing fire, in which case the team has to stay behind, while the protagonist advances to cover them. Throughout the game there are also several car chase sequences and shootouts. Gun combat is occasionally interspersed by short fighting sequences, as well as moments when a door has to be breached open in order to shoot the enemies down. The game is oriented towards co-operative gameplay, as the player is given optional objectives throughout its course.