Tony assumes the role of boss of the family after Junior is indicted on 12 RICO counts. Christopher begins selling phony stocks to senior citizens after getting a brokerage license from the SEC by paying someone else to take the test for him. Pussy is discovered alive and has a meeting with Tony. Meanwhile, Livia is still recovering from her stroke which brings Tony's older sister Janice in from Seattle and Carmela wants Tony to go back to therapy, the only problem is that Dr. Melfi does not want anything to do with him and will not refer him to another psychiatrist.

Tony plays both ends against the middle in a construction dispute, while Pussy has a revealing meeting with an FBI agent.
Livia becomes suspicious of Janice as she starts to get cozy.
Junior is released from jail, but finds himself working on a tight leash under Tony's thumb.

Jackie Aprile's older brother Richie returns to Jersey after being in prison for 10 years. However, Richie immediately dislikes the way that Tony is running the family and decides to have a chat with Junior. Meanwhile, Meadow throws a party a Livia's house and comes home drunk. Tony and Carmela disagree about how to punish her. Also, Dr. Melfi makes a visit to her psychiatrist Dr. Elliott Kupferberg.

Tony and the guys decide to make a visit to Italy as Carmela stays back at home and contemplates their marriage. While there, Tony finds himself attracted to Annalisa who happens to be the daughter of another mob boss. Angie Bompenserio 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 Nuovo Vesuvio Restaurant. All this upsets Christopher and Pussy. As time goes on, Tony becomes angrier than usual especially after finding out Janice and Richie, who used to be lovers, have reunited. Just as Tony is about to lose it, Dr. Melfi calls him up and asks him if he would like 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. However, he does admit that he does a have a slight problem with 'happy wanderers' who haven't a care in the world. He soon has to organize the 'Executive Game', a high stakes poker game that his father and Uncle Junior started over 30 years ago. Things go awry when Richie shows up unannounced. Meanwhile, Meadow is upset after Tony gives her a Jeep that he took in the poker game and Janice tells Richie that he has to start standing up to Tony or he will come to regret it.

After A.J. crashes his mother's car and begins denouncing God and the Catholic Church, Tony has about had it. However, Dr. Melfi tells him that it's natural for him to act this way at his age and that he has finally discovered that he is the one responsibly for all his actions. Pussy has been asked by the Feds to wear a wire to A.J'.s confirmation Meanwhile, Christopher once again has been slacking in his responsibilities and Tony is more than upset when he finds out he has been hanging out with a filmmaker instead and he asks him to make a choice immediately.

Carmela is concerned that Meadow might not get into a good college despite her wonderful grades and SAT scores and asks the twin sister of her neighbor Jean Cusamano to write Meadow a letter of recommendation since she is an alum of Georgetown Law School. Richie decides to give Tony a leather jacket that means a lot to him in the hopes he can get in good with the boss. Meanwhile, 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 saw Hell. Carmela informs Tony that she has had more than enough of him coming home with his shirts smelling like of perfume and she wants him to end it with his goomah. Meanwhile, Dr. Melfi is finding it increasingly difficult to cope with her disgust for Tony's 'profession'.

A witness knows that Tony was there when Matt Bevilaqua was whacked, which makes Tony realize if he does not find the person, he will have to leave New Jersey. Tony and Richie Aprile work together to collect Davey's gambling debt. Pussy is contacted by Agent Lipari about Bevilaqua's passing. 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 passing. Dr. Melfi takes to drinking vodka before each of her sessions with Tony. Richie and Junior decide to use their garbage routes to sell cocaine. Meanwhile, Junior is more than fed up with his house arrest and tries to contact his ex-girlfriend Roberta Sanfilippo.

Richie finally pushes Tony to the limit and Tony begins to plan for his removal.
Tony finds that breaking up with his Russian girlfriend is more complicated than he thought.
Janice takes matters into her own hands after a quarrel with Richie.

Tony is stricken by a nasty bout of food poisoning and has a strange dream conversation with Pussy in his delirium. When Tony wakes up, his suspicions are aroused.
The FBI catches Livia at the airport with incriminating evidence against her son. The Feds decide to move against Tony just before Meadow's graduation.