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The second season premiered on June 21, 2005. It began with Tommy at a new firehouse on Staten Island and his replacement at 62 Truck, Sully, becoming everyone's favorite. Sully leaves after the crew finds out that he likes to wear women's clothing and shun him. This clears the way for Tommy to return. Back in the old house Tommy shifts his focus to finding his family and dealing with his father, who took an unannounced vacation and came home with a new (rich) wife, Jenny Ng. Sheila has a miscarriage, but lies about it to keep Tommy near.

Meanwhile, Tommy and Johnny Gavin find out that their father had a long going affair during their childhood, which produced two children. Soon they suspect their new-found brother, a priest, is a pedophile. Mike stalks his ex-girlfriend. Chief Jerry's wife gradually deteriorates from Alzheimer’s and he is forced to seek help from his estranged son before placing her in a long-term care facility. Laura and Franco begin dating, but Laura eventually leaves Franco and the firehouse. Lt. Shea is conned by a prostitute, resulting in him losing his entire life savings. Jenny Ng dies, and Tommy's estranged sister Maggie shows up.

Tommy and his family reconcile for a time, but when their only son Connor is killed by a drunk driver it's too much for Janet to handle, and she blames Tommy. It only gets worse when Johnny finds out the driver may not do time, so Tommy's uncle, Teddy, murders him in public.