Carl Johnson and Ryder attempt to recruit B Dup during the mission Cleaning the Hood to kill some Ballas drug dealers. Dup turns them down as the Ballas are responsible for bringing the drugs into the city which he does not want to fight against, and is more concerned with making money by selling drugs.
Much later in the game, during the mission Beat Down on B Dup, Carl and Sweet visit Dup in his new home in Glen Park, Kilo Tray Ballas territory. After Carl and Sweet retake Glen Park, they enter Dup's house to face him. Big Bear cannot take anymore abuse from Dup so he punches Dup and left with Carl and Sweet. Dup isn't seen again after that though it is likely that he is still alive.
B Dup works for Big Smoke as he refers to him as "the boss" during the mission "Beat Down on B Dup". It is likely that Big Smoke supplies him with drugs.