Tommy is an alcoholically-charged emotional wreck after spending several months trying to track down his wife, who has kidnapped his three children. He is also dealing with the burden of a brand new crew of firefighter teammates and empregnating his cousin's widow.
Tommy discovers the whereabouts of Janet and their kids, but he must join his new station's babershop quartet. While the old house begins to take a shine to newcomer Sully, Lou and Chief Reilly try to figure out a plan to get Tommy back into the fold. Meanwhile, Mike's girlfriend Teresa breaks up with him, sending him into a emotional tailspin.
Chief Riley and Lou face resistance when they try to coax the firehouse into bringing Tommy back into the fold, until a major fire unearths a secret about Sully. Sheila has trouble opening up to Tommy about the baby, and Mike becomes possessive about his former girlfriend. Meanwhile, Tommy's dad returns from traveling the globe, with a new wife and a new outlook on life.
Tommy asks Mickey for help in deciphering the visions of Jesus and Mary he's constantly seeing now that he's no longer drinking. Tommy also finds himself in a dangerous fire situation when Chief Reilly and Mike the Probie have a communication breakdown. Laura finds herself in an ongoing argument within the station house and is soon shown the ropes on how men work together. Meanwhile, Tommy is startled by an unlikely appearance from Teddy.
Tommy begins to think his dad has another life he is unaware of after a priest gives him some private information. With Colleen back home, Tommy tries to get his other kids back, but must also contend with the erratic, secret behavior of Sheila.
Lou meets a terrible man who had his life saved due to Lou's part as an FDNY bone marrow donor, and wishes he hadn't donated at all. Sean learns that his new girlfriend is a serial fireman dater and begins to rethink his feelings for her. Tommy looks into the story of Sheila's pregnancy and continues the efforts to get the rest of his kids back home. Meanwhile, Franco risks harming his daughter's life when his reliance on painkillers deepens.
Tommy decides to sit by the side of a boy, laid up in a bed after being extensively burned in a fire. Meanwhile, Lou designs a plot to get his old girlfriend to reconnect with him and Chief Reilly is overloaded with unnerving details about his gay son's love life.
Chief Reilly brings the house over to the birthday party of his son's boyfriend, the result of which turns out to be more than he bargained for. Laura learns a terrible secret just as her relationship with Franco begins to deepen. Meanwhile, Tommy's family life could be jeopardized when he is attracted to the wrong, as in taken, woman.
Tommy uneasily slips back into a relationship with Janet. Franco uses the crew's assistance to try and reignite the spark with Laura. Meanwhile, a near-fatal accident on the job has Tommy rethinking his core beliefs.
Trouble ensues when Tommy, Johnny and Mickey do some digging into Father Murphy's personal life. Meanwhile, Laura suspects that someone in her crew has feelings for her and Tommy gets caught up in the escalating drama between Sheila and her girlfriend.
Sheila is adamant that Tommy explain to her son why becoming a firefighter is a bad life decision. Tommy must also go the distance to show his hockey team that he's still as tough as ever. Meanwhile, Franco tries to make Laura jealous, but his blind date is less than the attractive companion he expected.
Mike tells Sean about a health issue he's been coping with, and Chief Reilly braces for the worst period of his wife's illness. Tommy's estranged sister returns to the fold as the Gavins prepare to read off Mrs. Ng's will. Meanwhile, as Tommy and Janet continue with plans to reunite, they are suddenly faced with the tragic death of their son.
Tommy's need for retaliation against his son's killer begins to deepen, as Janet's sees her plans for a rekindled marriage dashed. Jerry finally takes the necessary steps for his ailing wife, and Sean begins to question his faith in the aftermath of Connor's death. Meanwhile, the station house finds itself shaken by some additional news.