Jones is in charge of the player's squad, and as such can be seen in every mission. Jones is first seen in the mission Back in Business, standing in the center of the squad. He also teaches the player how to move, crouch, use grenades and use their weapons in the guise of a "practice run". Jones can usually be seen at the beginning or end of a mission when the squad has regrouped, though occasionally the player will cross paths with him during a mission, such as when they must protect Franky as he drags Jones to safety. Jones is also teamed up with the player in the mission Underground Compound, where he and Dozer follow the player in an attempt to secure a Nuclear weapon.
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After chasing down Abu Bahaa in a Humvee with the rest of the squad, Jones moves in with the rest of the squad to capture him, but turns around and betrays the squad, shooting Dozer with his MP5 and taking Fox hostage. He pleads with the player to surrender to Abu Bahaa, but is killed by the player instead.