In 1991 Brooklyn, underboss Robert "Bobby Two Times" Valenti tries to keep the Gallo crime family stable while dealing with the loss of his wife Elena. As tensions rise with the rival Lazzaro family and the Gallos begin working with the Balkan organization led by Slavko Pavlić, Bobby is forced to balance loyalty, leadership, and survival. The season follows Bobby as he manages a family full of different personalities, from the unstable Tommy Brullo returning from prison, to the struggling Artie Rivieri, the loyal Danny Brullo, the sharp-tongued Aaron Conaro, and the young Gabe Pavlić entering the organization. As Tommy's reckless actions threaten the family's future, Bobby is forced to make choices that test his relationships and change him forever.

After the events of Season 1 and Tommy's execution, Bobby and the crew are under surveillance by disgruntled FBI Agent Albert Chung, putting pressure on both the freight operation with the Balkans and also the family's stability itself. A new faction arises in Sunset Park, led by the charasmatic and cunning Juan Campa and his level headed right hand man Ivan Cortez.