Brotherhood, set against the desperate worlds of politicians and mob bosses, looks at how gray good and evil can be. Two brothers on opposite sides of the law, determined to protect the neighborhood and what is theirs by whatever means necessary. Placed in a fictional Irish neighborhood in Providence, Rhode Island, the series explores what lengths people go to achieve the elusive American dream.
Freddie Cork threatens to whack Michael unless Tommy throws state contracts Freddie's way. Meanwhile, Michael gets into a beef with Moe Riley, one of Freddie Cork's underlings, who is currently in control of Michael's old turf. Eileen Caffee, Tommy's wife, has secrets of her own: she meets Carl, an old boyfriend, at a local motel, where they smoke dope and have sex. In the end, Michael achieves a tenuous treaty with Freddie.
Defying Freddie's direct orders, Michael and his old partner, Pete McGonagle, intimidate a local merchant into selling them her store for half its worth. When the merchant goes to Tommy to complain, Tommy passes her off to police detective Declan Giggs, who used to date Tommy's sister in high school. Declan compromises himself when he makes the complaint go away. Tommy's efforts to stop the new highway, including a deal with the mysterious power-broker Judd, lead him to bribe and blackmail two of his fellow representatives. The conflict between Eileen's public demeanor and private pain is temporarily halted when she learns that her sister-in-law is having medical problems.
A local garbage strike puts Tommy in the difficult position of mediating between the garbage collectors' union, controlled by Freddie Cork, and the mayor of Providence. To end the strike, he is forced to surrender a piece of his independence to Judd. Eileen struggles to pull out of a tailspin after her lover Carl ends their illicit affair. Michael's continuing effort to expand his criminal activities is thwarted when he discovers that his old gang has lost its teeth - and that he and Pete are on their own. He's further disappointed when he goes to visit his old girlfriend Kath Parry and finds that she's married with two kids. In the end, Michael's frustration explodes in the wrong place - at the wrong time - in front of the wrong person - his eight-year-old niece, Noni.
Tipped off by Moe Riley, Treasury agents who are looking for Michael's counterfeit currency raid Rose Caffee's house during Sunday dinner, while the entire family is present. The agents don't find the currency, but bad publicity generated by the raid causes the Speaker of the House to kill an important real estate deal that Tommy desperately needs. To survive, Tommy is forced to pledge his loyalty to the Speaker. For Tommy's oldest daughter, Mary Rose, the raid initiates a growing fascination with her dangerous uncle, Michael. In revenge for the raid, Michael frames Moe for murder.
When Freddie Cork refuses to let Michael and Pete play on his softball team in a local bar tournament, Michael goes out and takes over his own bar. When the two teams meet, tensions rise. Rose discovers firsthand the destructive power of globalization; as a shop steward for her union, she loses a fight to stop layoffs within her factory and is herself fired. When the Speaker proposes a new waste-disposal station in Tommy's district, Tommy plays fast and loose to make sure his constituents are properly compensated. If along the way, a few extra dollars end up in his own pocket, so be it.
When Declan and Ralph mistakenly shoot an undercover federal agent, Michael steps forth to help them get rid of the body. Though Declan and Ralph get away clean, their partnership is now contaminated. Tommy's embarrassed that he had to borrow money from his in-laws and sets out to pay them back. Using his political pull with the zoning board, Tommy lands himself a hefty real-estate commission. Eileen's drug and alcohol abuse gets out of hand and causes her to abandon the family cat out in the woods. Guilt-stricken, she returns to retrieve the cat and is arrested for erratic behavior. Forced to bail her out, Tommy can no longer deny the problems in his marriage. Mary Rose finds a joint in Eileen's pocket and can't resist trying it. When her uncle Michael catches her, her fascination with him only intensifies. She ends up working in his liquor store after school.
When the owner of Tommy and Michael's childhood movie theatre ends up in debt to Michael, Michael convinces Tommy to help save the theater from the wrecking ball. Tommy agrees, on the condition that Michael have nothing to do with the big benefit Tommy organizes. Michael sticks by the deal, but Freddie Cork steals the fundraiser proceeds and the theater is forced to close. Michael's sidekick Pete falls off the wagon; Michael helps get him back into AA. In the throes of a deep depression, Eileen confesses all her sins to a startled Mary Kate, who urges her to get psychiatric help. Meanwhile, Rose starts a new job in a big box outlet store and realizes the powerlessness of the contemporary American non-union worker. Corrupt union boss Marty Trio (TOM KEMP) confesses to Declan that he has cancer. Declan tries to turn him as a witness but Marty refuses.
Michael takes his old girlfriend Kath Perry on a milk run to New Jersey to pick up some money for Freddie. When the plan goes awry, Michael resorts to what he knows best - violence. Kath sticks by him, and he realizes how much he cares for her. Sensing Michael drifting away from her, Rose goes overboard in planning a surprise birthday party for him, only to be angered when Michael shows up with Kath in tow. Determined to stay sober, Eileen fends off her demons as best she can, but the stress proves too much. She falls off the wagon and is caught drinking by Pete. The Speaker tumbles in a scandal, so Tommy plays on the insecurities of the new Speaker to get himself promoted to Majority Leader - the number two position in the House.
A bus loaded with people from "The Hill" crashes while returning from a Patriots football game. The accident is caused by a suicide-jumper, leaping from a highway overpass. The jumper was Freddie Cork's oldest son Ricky. Freddie enlists Tommy to get Ricky a proper Catholic funeral. Michael discovers that Ricky was gay. He uses this information to manipulate Freddie, who, in a rage, then kills Ricky's lover. Also victims of the crash are Eileen's erstwhile lover Carl Hobbs and Marty Trio's wife Leanne. Carl's death makes Eileen want to atone for her sins. Leanne's death convinces Marty that he should turn state's evidence.
Neil Caffee, Tommy and Michael's father, turns up and threatens to sell Rose's house out from under her unless his sons help him out of a $200,000 financial jam. Tommy and Michael have only one goal: to get Neil out of their lives forever. This time, it's Tommy who loses his temper and turns to violence. Michael stays cool and gets the job done. Pete and Eileen have their own secret little AA meeting. Pete falls off the wagon after Michael orders him to kill a fourteen-year-old drug dealer - so now it's Eileen who comes to Pete's rescue. Rose finds herself ostracized by her friends because of Michael's growing criminal activities. For the first time, Rose admits to herself what Michael does for a living and confronts him about it. Tommy is furious when he discovers Mary Rose working at Michael's liquor store. Whatever goodwill was won by their joint effort to get rid of Neil is now gone.
Fresh from jail, Moe Riley is ordered by Freddie Cork to kill Michael by the end of the big Irish wedding. When Tommy discovers this, Freddie threatens to expose Tommy's corruption if he warns Michael. Tommy begs Michael to leave but won't say why. Michael refuses. Declan realizes his boss has told Marty Trio to get Tommy on tape saying something incriminating. Declan warns Tommy, but feels so guilty that he gets rip-roaring drunk. Eileen has a wonderful time at the wedding, drinking, smoking pot, flirting, but a chance encounter changes her perspective on everything. Finally, in a drunken rage, Declan confronts Michael when he catches Michael slipping a bribe to his partner Ralph.