Season 3 begins with Tommy experiencing mounting frustration with his diminished role as Speaker Donatello's factotum and considering a career change. Meanwhile, Michael learns that Freddie Cork is getting out of prison, which has a serious impact on his relationship with Attorney General Franklin. And with her birthday approaching, Rose tries to cover up her deteriorating health.
Tommy hopes to use his newfound leverage to gain the mayor's support for a waterfront-development project, while Michael's involvement with the Nozzoli crime crew could cause problems for Tommy. Elsewhere, Attorney General Franklin disappears, just as Declan commences his statehouse corruption investigation; Eileen's pregnancy keeps her from a promotion at work; and Rose seeks answers about her mysterious illness.
Tommy deals with the aftermath of a fire that claimed a fireman and some Latino squatters; Declan picks up a promising new lead into his probe of statehouse corruption and brings in a second investigator; Moe's violent temper lands him in hot water, and Freddie is his only way out of the mess; Colin's infatuation with Kath, Michael's girlfriend, impacts his work.
Despite Tommy's plan to enter a new profession, Eileen fears that he won't be able to get politics out of his system; hoping to heal the rift in their rocky marriage, Declan and Cassie go on a romantic weekend getaway that doesn't turn out as planned; Michael becomes increasingly paranoid after a troubling incident at a Nozzolli barbecue, and he also becomes concerned when he's unable to find Kath and Colin.
Declan moves to build a solid case against some corrupt local politicians, which triggers panic at the statehouse, so Tommy attempts to subtly pump him for dirt on the investigation; Rose gets a diagnosis on her health problems and shares it with Eileen; tensions increase between Michael and Colin as they plan a heist with Freddie.
Eileen's concerns about getting the family off the Hill are compounded when Speaker Donatello seeks Tommy's help passing a new budget; Declan uncovers a connection between Tommy and the waterfront project, as well as a possible link between Tommy and Nozzoli; Michael takes offense to Rose's close attachment to Colin.
Colin and Kath fear Michael's reaction if he were to uncover the truth about their relationship; Eileen's problematic pregnancy confines her to bed and it's making her stir-crazy; with investigative waves being made over the waterfront project, Tommy goes to Michael for help.
With Donatello in critical condition, Tommy appears to be next in line for Speaker of the House, which leads Freddie Cork to try to get in his good graces; Italian mobsters, the state police and the Feds are on Michael's trail while he tries to track down Colin.