When a retired gay firefighter makes a published claim that several firemen who died in 9/11 were closeted gays, Chief Reilly is determined to set the record straight. While attempting to mask the pain of losing his wife and kids, Tommy does Jimmy a favor and spies on his widow which leads to a surprising discovery. The probie must deal with the unexpected repercussions of being a hero after making his first save in a fire.
When Tommy struggles to help Janet in a financial crunch, he must turn to his Uncle Teddy to help him out. The new female addition to the house fights to be accepted by the guys while they do everything they can to drive her nuts. Just as Mike is getting fed up from sleeping on the firehouse couch, he is offered a helping hand with a free place to stay... at a steep price.
When Janet needs more money to cover house repairs, Tommy turns to Uncle Teddy and his "little" friend to help him out with extra cash. When Franco's father has a stroke, Franco finds himself trying to juggle work and raising his daughter on his own. Meanwhile, a goodwill tribute to the firefighters lost in 9/11 goes awry and the firehouse is put in jeopardy.
The hockey game rematch between the NYPD and the FDNY is right around the corner and Tommy must figure out a plan to save himself from being pummeled by the cops who have it out for him. Tommy's relationship with Sheila is discovered by the guys and they must adhere to tradition to handle it in their own way. When Tommy is visited by his demons during a fire, Franco comes to his aid... with devastating results.
In the opener to the second season, troubled Tommy Gavin is having a difficult time adjusting to life at his new uneventful firehouse after the volatile split with his old crew. On top of this he is still looking for his missing wife who has kidnapped his three children and he has to come to terms with the fact that his dead cousin’s wife is pregnant with his baby. His frustrations come to a head and he has a meltdown with a street vendor selling 9/11 memorabilia.
Jerry forces the crew to attend a birthday party that his son is throwing for his boyfriend. Meanwhile, Tommy makes a move on Mariel after she tells him she might not be his half sister after all. Franco asks Laura to move in with him while Sheila tries to make Tommy jealous by showing off her new girlfriend.
During a night out, Franco and Tommy meet two women. Tommy is finding himself bribing his daughter Colleen before she tells their mother about his indulgent treatment of her sister Katy. Jerry visits his wife Jeannie in her expensive nursing home and soon goes to Lou for financial help. Meanwhile John Sr. insists on having his 83rd birthday at a restaurant that no one else likes.
Franco begins to fear he's becoming Alicia's boy toy, while Tommy finds a way to end the fling between Damien and his science teacher. The rest of the crew also face their own problems - Lou is becoming real unstable emotionally, the chief has financial problems, and Sean is afraid of Tommy finding out who he's been sleeping with.
The crew decide to save some children from a disabled school bus as they go to call in Harlem. However, the soon meet up with an upset Rev. Al Sharpton. Franco finally realizes why Alicia is so interested in him. Mike and his roommate discuss their sexuality. Sean ends up telling Tommy about his feelings for Maggie. Sheila has a proposal for Tommy. Janet wants to talk to him about their settlement, but with no lawyers involved.
After a game of street hockey, Sean takes some sleeping pills believing they are painkillers and it has an unwanted consequence. In the meantime, Tommy and Angie decide to go on their fake date that they know will upset Janet. After having a close call, Lou gets a new angle on firefighting from his Uncle Red.
While Tommy and Johnny have another encounter, Janet and Angie re-establish their acquaintance. Meanwhile, Sheila is unhappy when she sees Tommy and Angie together. Maggie wants to get back together with Sean. Mike hooks up with a woman at a bar, making his roommate, Chris, jealous. Franco finds out about Jerry's second job at the pub, and the money in the no-smoking jar goes missing.
Janet has given birth to a baby boy---whom she fears prefers Tommy to her. But Tommy has a bigger problem: He's suspected of starting the beach-house fire. Meanwhile, Jerry's son asks him to be his best man at his commitment ceremony; Richie wants Franco to marry Natalie; Lou and Theresa get distracted in church; and the volunteer firefighter (Jennifer Esposito) who rescued Tommy from the beach house takes an interest in him---and isn't shy about letting him know.
Sheila lies to Tommy when he confronts her about the beach-house fire. But they present a united front to the insurance investigators, as embarrassing as it is for Tommy. Meanwhile, Lou is determined to get a basketball ringer (Larenz Tate) to be 62 Truck's new probie; Uncle Teddy is released from jail; Colleen runs away with her rock-musician boyfriend; and Mike's mother has a deathbed request.
Tommy encounters Colleen's boyfriend and sparks fly; Jerry learns he flunked his physical and is given a desk job; Uncle Teddy, hiding from Ellie, breaks into prison guard Lenny's apartment; Sheila goes out with the man who pulled her from the beach house, while Tommy keeps avoiding Nona (Jennifer Esposito), the volunteer firefighter who rescued him from the blaze; and Mike seeks Tommy's advice on how to deal with his dying mother's request that he kill her.
The firehouse gets a new chief (Jerry Adler), who is rumored to possess a very special gift; Tommy suffers embarrassment during a hockey game against the NYPD; Franco works up the nerve to propose to Natalie while Sean tries to talk Maggie out of a divorce; and Sheila makes a surprising proposition as Janet's depression deepens.
A devastating fire has a profound effect on the crew; Tommy wrestles with his feelings about the baby; Alicia (Susan Sarandon) returns with a proposition for Franco; Troy breaks up with Sheila while Lou makes a tough decision about Theresa; and Sean apologizes to Mike about the fire he set that burned down Mike's mother's house.
In the fourth-season finale, Sheila learns that Jimmy's ghost has been spotted on several occasions, so she investigates. Meanwhile, Colleen blames Tommy for her failed relationship; Franco and Natalie come to an understanding, as do Lou, Cousin Mike and Latrina; and Tommy spends time with his father.
Tension runs high as Needles holds the guys accountable for their lack of judgment. Tommy steps up and takes responsibility for Damian's future in the firehouse. Sheila provides Tommy with an oasis as a sign of her gratitude but it may not be enough to save him from the wrath of Mike, Dwight, and the ghosts of Tommy's past.
Needles' political leverage catches HQ off guard, leaving them no choice but to reopen the house. Feinberg loses control, Damian saves a helpless victim, and Tommy and Sheila find themselves in hot water.
Tommy and Sheila find themselves in hot water with Janet and Mickey and realize the truth about their own relationship. Damian attempts to leave the crew, but is seduced back by the camaraderie of the brotherhood.