Season two centers on a federal housing project in the Roxbury neighborhood of Boston that is plagued with drug violence and a rightful distrust in local law enforcement. As coalition leader Grace Campbell works tirelessly on behalf of the community, her efforts are undermined by gang activity happening right under her nose. Enter irreverent FBI agent Jackie Rohr, who is here to exploit Boston's defective criminal justice system in a desperate attempt to salvage his own career.
When an assistant U.S. attorney overdoses and ends up left for dead, Decourcy Ward suspects Jackie Rohr's involvement. Jackie, in turn, goes after the BPD for a questionable drug arrest at Braxton Summit, a federal housing project. Community activist Grace Campbell recruits Siobhan Quays to work on behalf of Braxton and its residents, but their efforts are subverted as tensions flare between rival gangs.
As Decourcy increases pressure on the Justice Department, Jackie counters by looking into his adversary's romantic past. While Jackie's digging up dirt, Siobhan is planning ahead, focused on starting a family even as Decourcy remains preoccupied by the escalating conflict. Jenny realizes she can't keep ignoring her mother after an unsettling phone call. With business at the salon all but dead, Cathy Ryan turns to an unlikely income source.
Jackie uncovers one of Decourcy's informants and hatches a plan to use him as a pawn to discredit the assistant district attorney. Decourcy stops by the Rohr house, hoping to get something out of Jenny that he can use against her husband. Siobhan receives some welcome news, in the midst of plotting her run for City Council. And her client, Kelvin Campbell, is released from custody, though he can't free himself of what happened on Valentine's Day. Jimmy Ryan, meanwhile, faces problems far worse than a guilty conscience.
After seeing Holly in the ICU, Jackie reckons with the destructive consequences of his actions, as Rickey Townsend prepares to testify against Decourcy. With violence intensifying between the Copeland Crew and the Braxton Boys, Decourcy, Anton and Siobhan face off in the interrogation room. Grace, left reflecting on her role as a mother and leader in the community, makes an unfortunate miscalculation. And back at the Rohr house, Jenny makes fast friends with the mysterious woman from Belfast.
As U.S. Attorney Karen Shimizu tries to get rid of her troublesome agent once and for all, Jackie schemes his way into a new mission. At the Suffolk County Courthouse, Decourcy and Siobhan spar on opposing sides of a legal battle. Meeting dead-ends at every turn in the effort to help her son, Grace does something desperate. With a nudge from Maeve, Jenny surprises Benny with some rebellious fun. On the other side of town, Cathy re-ups her supply by going straight to the source.
With Anton on the lam, Kelvin struggles to lead the Braxton Boys and Jackie homes in on Grace. He knows she's hiding something. Sidelined from the investigation, Decourcy finds himself at a disconnect with Siobhan, as he seeks vengeance and she focuses on recovery. When Cathy's arrangement with Isaac falls through, she pays a reluctant visit to old friends for help. Jenny, meanwhile, finally uncovers the truth about her new friend.
Assuming the involvement of the Campbell brothers at the Copeland territory shootout, Jackie confronts Grace, who can no longer sidestep her sons' criminal activity. She is forced to make a terrible compromise. Resenting the outcome of a negotiation that he could not take part in, Decourcy finds comfort in the strength of Siobhan, who keeps her head even after tragedy strikes. Jenny insists on helping Maeve, whether or not that means defying Jackie.
As Boston mourns another loss, Decourcy pursues justice in and out of the courtroom. Despite his maneuvering, Jackie discovers that he can't escape his past, while Jenny decides to finally confront hers. Cathy says goodbye to the root of her struggles. Siobhan sets her sights on a new dream.