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Season 3
The third season began on May 30, 2006. Tommy and Janet are now re-separated and Teddy is in jail for murder. Janet begins sleeping with Johnny, Tommy's brother. Tommy and Johnny fight it out in the street, and, later, following an argument, Tommy and Janet have a very physical sex scene. The violence of the act is contrasted with his post-coital attitude and the suggestion that she may have enjoyed it.

Meanwhile Lt. Shea, still smarting from getting conned, is becoming testy with everyone on the crew and slowly spiraling down. The Probie (Mike) begins a sexual relationship with his (male) roommate and Tommy falls back into things with Sheila, Jimmy's widow. Sheila wants to get Tommy back and begins to drug him to have sex. Maggie soon finds herself dating Sean Garrity, among others.

Janet gets pregnant with either Johnny's or Tommy's baby and wants to have it to replace Connor. The crew finds out about Probie's possible homosexuality and Tommy comes to his defense. Franco starts to date Alicia (Susan Sarandon), a rich older woman who eventually takes his daughter from him (he is unable to do anything about it because he had taken her from foster care without permission and therefore is not the girl's guardian anyway). Lt. Shea moves in with Tommy and begins seeing Teresa, a soon-to-be ex-nun with whom he plans on moving to Florida to be first mate on his cousin's boat. Chief Reilly tries to meet his wife's increasing health care costs by taking a second job at a bar. Later he suffers a heart attack after having sex with Karlene, an illegal immigrant who cares for his wife.

During a stakeout, Johnny is shot three times through the back and killed by someone who was contracted to kill him to stop him from testifying against a powerful drug dealer. During his funeral Sean and Maggie decide to get married at the cemetery. Rosemarie Gavin is also introduced, the long lost sister of Tommy, Johnny, and Maggie. She is deaf and had been shunned by her parents but reconciles with her father.

With the house seemingly breaking up Tommy decides to retire and move in with Sheila. He changes his mind after talking with Janet about her pregnancy and hearing that Mike isn't transferring, Lou has changed his mind about the boat (after discovering he lacked "sea legs") and Franco has failed a lieutenant's exam.

While at Sheila's new house he tells her he is not retiring from the FDNY. Distraught, she drugs him and accidentally starts a fire. The fire is able to spread while Sheila is overwhelmed by frustration, and the finale closes without making it clear if Tommy made it out of the house.