Tony assumes the role of boss of the family after Junior is indicted on 12 RICO counts. Meanwhile, Christopher begins selling phony stocks to senior citizens, Pussy is discovered alive, and Livia, recovering from her stroke, is visited by Tony's older sister, Janice.
Pussy gets a visit from FBI agent Skip Lipari and ends up becoming a rat for the Fed's case against Tony. Meanwhile, Livia is convinced that Tony and Janice are planning on getting rid of her ... literally, whilst elsewhere, Junior gets out of jail on a medical release.
Jackie Aprile's brother, Richie, returns to Jersey after being in prison for 10 years. However, Richie dislikes the way that Tony is running the family and decides to have a chat with Junior. Meanwhile, Meadow throws a party at Livia's house and comes home drunk.
Tony and the guys decide to visit Italy, but Carmela stays home and contemplates their marriage. While there, Tony finds himself attracted to Annalisa who happens to be the daughter of another mob boss. Meanwhile, Angie tells Carmella that she wants to divorce Pussy.
Furio Giunta, the newest member of Tony's crew, has arrived from Italy and thanks to Artie Bucco is now the head mozzarella maker at the restaurant - which upsets Christopher and Pussy. Meanwhile, Dr Melfi calls Tony and asks him to resume his therapy sessions.
Tony decides to lie to Dr Melfi and tells her that everything in life is fine - but she knows better. Meanwhile, Meadow is upset after Tony gives her a Jeep that he won in a poker game, and Janice tells Richie he has to start standing up to Tony for his own good.
After AJ crashes his mother's car and begins denouncing God and the Catholic Church... Tony is reaching breaking point. Meanwhile, Tony also discovers Christopher has been slacking again, avoiding his duties and hanging out with a filmmaker instead.
Carmela is concerned that Meadow might not get into a good college despite her wonderful grades and SAT scores. Meanwhile, Richie tries to schmooze Tony by giving him a leather jacket he knows he's fond of, and Christopher gets caught in the crossfire outside a diner.
Christopher survives the attempt on his life, although he tells Tony and Paulie that he almost died and caught a glimpse of his afterlife. Meanwhile, Dr Melfi is finding it increasingly difficult to cope with her disgust for Tony's "profession".
A witness knows Tony was there when Matt Bevilaqua was whacked, which makes Tony realise if he does not find the person he will have to leave New Jersey. Meanwhile, Carmela becomes close to her new wallpaper guy who happens to be Davey's brother-in-law.
Tony gets warned that the Feds are still planning to come after him even though he's been cleared for the Bevilaqua death. Meanwhile, extremely unimpressed with his house arrest, Junior tries to contact his ex-girlfriend Roberta Sanfilippo.
Tony tries to break off his ties with Richie and Irina, and even goes so far as to asking Dr Melfi to find a therapist for Irina; so Richie decides it's time to make his move on Tony. Meanwhile, Janice has also had more than enough of Richie's ways.
Tony is thrilled Janice and Richie are out of his hair, so he plots to get rid of Livia as well. Meanwhile, after a plate of bad food, Tony has erotic hallucinations about Dr Melfi and also one of Pussy as a fish, which convinces him that Pussy has gone to the Feds.