Season three of Brotherhood continues the blue-collar saga of Providence, Rhode Island native sons Michael and Tommy Caffee. After winning his closely contested re-election campaign, Tommy is left as a subordinate to Speaker Donatello, which makes him contemplate leaving political life altogether. As for Michael Caffee, his precarious position as boss comes under siege as he is slowly overwhelmed by ever-building paranoia.
Tommy's frustration with his new role as Speaker Donatello's errand boy leads him to consider a risky career change. With Michael still refusing to speak to Tommy, Colin arranges for both brothers to attend Rose's birthday party. Rose tries to hide her deteriorating health. Eileen struggles to meet the demands of her growing family while becoming more invested in her job at Social Services. Michael's relationship with Attorney General Franklin starts to unravel when Michael hears that Freddie Cork is getting bail. To avoid serious outside scrutiny, Tommy asks Declan to run a special investigation into corruption in the state house. Declan accepts, looking for real justice.
Tommy uses his new leverage to convince Mayor Panzarella to get behind the Waterfront development. At the same time, Michael's business dealings with Nozzoli create a new roadblock for Tommy. As Declan starts his investigation into state house corruption, Franklin's sudden disappearance draws attention. Eileen gets passed over at work because of her pregnancy as Rose tries to get answers about her mysterious illness.
Tommy struggles to do the right thing after a fire in an abandoned mill kills a firefighter and several Latino squatters. Declan brings in a second investigator to help him work a promising new lead. Colin's torch for Michael's girlfriend, Kath Parry, begins affecting his work. Moe's hot temper gets him in trouble and only Freddie can protect him.
Labor Day Weekend. Tommy surprises Eileen with a concrete possibility for their new life away from The Hill but Eileen worries that Tommy won’t ever give up politics. Declan and Cassie go away for a romantic weekend only to find themselves faced with the difficult realities of their rocky marriage. An incident at Nozzoli’s barbeque pushes Michael’s growing paranoia into overdrive. The conspicuous absence of Kath and Colin does little to ease his mind.
Declan's push to build a case against corrupt local politicians sends up red flags in the State House and Tommy tries to charm him into sharing information about the investigation. Rose discovers the truth about her health and confides in Eileen. Tension builds between Michael and Colin as they help Freddie plan a heist.
Eileen worries that her family will never leave The Hill when Speaker Donatello draws Tommy back in to help pass the budget. Declan gets new information about Tommy’s involvement in the Waterfront Project and breaks some rules to find a link between Tommy and Nozzoli. Rose’s attachment to Colin fuels Michael’s anger and paranoia as he refuses to help Nozzoli get in on Tommy’s Waterfront contracts.
Kath and Colin worry about what Michael might be capable of if he becomes too suspicious of their relationship. Eileen goes stir crazy when her advanced pregnancy confines her to bed. Tommy asks for Michael's help as the investigation hones in on the Waterfront Project.
When Speaker Donatello's critical condition makes Tommy the heir apparent for the Speakership of the House, Freddie Cork maneuvers to get on Tommy's good side. With the Italian mob, the Rhode Island Police, and the Feds after him, Michael’s obsessive need to find Colin puts everyone in jeopardy.