A "friendly" date between Tommy and the widow of his dead cousin takes a unexpected turn when she makes a move on Tommy. Franco's ex-girlfriend shows up at the firehouse and claims he's the father of her five-year-old daughter, turning his life upside down.

Tommy comes to terms with the reality of his broken family as a result of a shocking experience with his father. When a freak accident occurs, Franco must make a life-changing decision, and Chief Reilly is forced to expose a family secret in order to save his career.

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.

While Tommy attempts to make reason of the chaos in his life, he continues to defy death while pulling dangerous stunts on the job. Lou admits his infidelity to his wife and receives an unexpected surprise. When tragedy strikes his family, Tommy must come to the rescue of his father.

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.

In an effort to get more time off to search for his wife and kids, Tommy joins the new firehouse’s Barbershop Quartet. Meanwhile back at the old station, Lou and Chief Reilly conspire to get Tommy back, but the rest of the crew has grown fond of his replacement.

Franco's addiction to painkillers has driven him to a support group to get help with his problem. A young boy clings to life after Tommy saves him from a fire. Jerry is introduced to his gay son's life partner.

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.

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.

The crew faces more than accustomed when rescuing a man from his burning apartment; Sean has a request for Maggie's dad; Franco thinks his new girlfriend is hiding something from him; and Tommy realizes that his crew's future together may be in jeopardy.

Following a meeting with Janet, Tommy has yet another confrontation with Johnny; Teddy's conjugal visits with Ellie prove to be a letdown; and Franco tries to befriend his new girlfriend's mentally challenged brother. Elsewhere, Tommy keeps his vigil at Stack's bedside.

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.

Emotions flare up when the crew learns about Jerry's death; Tommy's manhood is called into question after some embarrassing romantic encounters; and Lou resorts to blackmail to recruit Bart (Larenz Tate) as the new probie for the house basketball team.

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.

Tommy plays hero in someone else's uniform, confusing the crew; Colleen finds a new reason to get upset with Tommy; Natalie asks Franco for a favor; a rift between Mike and Black Shawn nearly leads to blows; and Tommy makes a move on the chief's daughter. This does not please the chief.

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.