Jackie Aprile's health worsens, forcing Tony to make a tough decision. Meanwhile, Anthony Jr. learns the true nature of his father's job in 'waste management.' Also, Tony hires sleazy police lieutenant Vin Makazian to investigate Dr. Melfi's background.

Uncle Junior enjoys a romantic tryst in Boca with his girlfriend Bobbi, not realizing that she's been gabbing to her beauty-parlor friends about his oral talents. Meanwhile, controversy arises when Meadow's soccer coach announces he's leaving the school.

Season Two opens with the aftermath of the federal crackdown: Junior's in jail, Melfi refuses to see Tony, Christopher's expanding into new business ventures, Pussy is still missing...and Tony's adjusting to life as the new boss. To complicate matters even more, Tony's free-spirited sister Janice arrives to take care of Livia.