At Uncle Junior's meeting with his capos, Jimmy Altieri makes it obvious to the boss that he is wearing a wire. Junior agrees to let Tony Soprano have him killed. Christopher Moltisanti takes Jimmy to a hotel for what he promises will be a night with two Russian women. But after they enter the hotel room, Silvio emerges from behind a door and shoots Jimmy in the back of the head. His body is later found with a rat stuffed in his mouth, sending a message that he had made a deal with the FBI.
In Tony's therapy session with Dr. Melfi, Melfi tells Tony that his dream (of Isabella) indicates his subconscious is alerting him to problems with his mother. Because Tony's life is in danger, Melfi suggests that his mother may have been involved in the decision to take his life. Tony becomes furious, breaks a glass table and attacks Dr. Melfi, holding her down in her chair. He tells her that they are finished and that she is lucky he does not "break her fucking face into fifty-thousand pieces."
Carmela Soprano and Rosalie Aprile have lunch at the re-opened Nuovo Vesuvio, Artie Bucco's new location for his restaurant that he opened with the insurance money he received after the original Vesuvio burned down. Father Phil Intintola drops by and sits with them. He discusses food and his watch, which belonged to Jackie Aprile but was given to him by Rosalie after Jackie's death.
FBI agents Dwight Harris and Grasso hold a meeting with Tony and U.S. Attorney Agent Cubitoso. The agents have Tony listen to recordings they made at Green Grove to attempt to convince him that his life is in danger and that his mother and uncle are involved. On the tapes, Tony hears Junior and Livia planning a hit on him and discussing Tony's visits with his psychiatrist Dr. Melfi.
Artie Bucco visits a bedridden Livia and brings her some food. Somewhat disoriented, Livia informs Artie that Tony burned down Artie's restaurant. Later, Artie confronts Tony with a loaded rifle outside Satriale's, outraged that Tony destroyed the place where three generations of Buccos worked. Tony denies that he started the fire. He says his mother is confused and senile. He swears "on his mother" that he did not incinerate the restaurant. Artie puts down the rifle and smashes the weapon on his own car.
At the Bada Bing, Tony informs Silvio, Paulie and Christopher he has confirmed that it was Junior who took out the hit on him. Paulie suggests that Junior may want to finish what he started, and Christopher points out that Junior would use his own staff to do the job. It is decided that Chucky Signore should be made to "disappear without setting off any alarms." Tony and Silvio pay Chucky a visit at a marina. After starting a conversation with Chucky about a large fish that he is carrying, Tony pulls a gun out of fish's mouth and shoots Chucky repeatedly. Silvio unloads cement blocks and chains from the car and he and Tony load the items onto Chucky's boat and cast off.
With the knowledge of his mother's involvement in the plan to take his life, an apologetic Tony arrives unannounced at Dr. Melfi's office and convinces Melfi to see him again and admits that she was correct about his mother. Tony warns Melfi that her life might be in danger. Melfi tries to give him pragmatic reasons why it would be unnecessary for any of Tony's enemies to come after her, but Tony tells her none of that matters. Later, when Tony shows up at her office again the cleaning staff inform him that Dr. Melfi is on vacation.
Artie visits Father Phil and consults with him about the anger and rage he is feeling towards Tony and life. He tells Father Phil he cannot tell his wife Charmaine about the fire because she would be distraught. Father Phil advises Artie to tell Charmaine and to turn in Tony to the police.
At the Bing, Tony tells Silvio, Paulie and Christopher about seeing a psychiatrist because of his issues with passing out and depression, and that Junior knows about the psychiatrist and is using the situation against Tony. Silvio doesn't mind the news, and Paulie admits to once seeking similar help himself because he had issues and "learned some coping skills." Christopher asks if it is like marriage counseling then seems upset and storms out.
At the church, carrying a bowl of pasta, Carmela pays a surprise visit to Father Phil, but observes Rosalie and Phil having an intimate discussion as he eats and praises the food that Rosalie has provided him. Carmela leaves without speaking to Father Phil and dumps the pasta in a trash can outside the church.
Charmaine hires Adriana La Cerva as a hostess at Vesuvio and tells Artie that she is very happy with the new restaurant. When Artie later sees Father Phil, he confesses that he never informed his wife because she is happy with the restaurant and is not expressing her usual negativity.
Mikey Palmice heads out for a morning jog. Paulie and Christopher eventually chase him into the woods where Mikey falls into a stream. Christopher confronts Mikey with the Brendan Filone slaying, while Paulie is angry because he believes that he has contracted poison ivy while running through the woods. Both men empty their guns into Mikey.
The FBI arrests Junior, capo Larry Boy Barese, underboss Beppy Sasso and thirteen others. A TV news reporter mentions that Mikey Palmice is missing and may have fled. Tony learns from his lawyer that he was not indicted because the charges relate to a telephone calling card scam and a stock scam in which he was not involved. Junior is offered a deal if he confesses that Tony is the de facto boss of the family, running the operation behind Junior's back, with the help of some New York families including underboss Johnny Sack. The Feds want the bigger targets in New York, but a prideful Junior stubbornly refuses to admit to this scenario about him and Tony.
Father Phil visits Carmela with a movie rental and asks about Tony, mentioning the indictments. Carmela points out that Father Phil is a hypocrite, judging Tony's lifestyle but enjoying Tony's food, entertainment center and time with his wife. The Father wonders if she thinks of him as a parasite. She accuses him of manipulating spiritually thirsty women, and mentions that food and sexual tension are part of his game. Crushed, Father Phil departs without saying another word.
Tony goes to Green Grove to confront his mother, picking up a pillow on the way to her room. However, he is informed by the staff that Livia has suffered a stroke. As Livia is being wheeled into the emergency facility on a gurney, and with her mouth covered by an oxygen mask, Tony discards the pillow but tells her he knows what she has done. When he perceives her to be smiling, he has to be restrained by staff.
In the final scene, a fierce rainstorm erupts and Tony is stranded in his car with his family, unable to reach their intended destination. Instead, Tony heads to the nearby Nuovo Vesuvio. Tony, Carmela, A.J. and Meadow hurry to the door where Tony asks Artie to let them in. Artie, who is preparing to close for the evening and has been cooking by candlelight without electrical power, reluctantly opens the door and allows them in, where they see Paulie (with calamine lotion on his face) dining with Silvio, as well as Christopher eating with Adriana. The Sopranos have a seat at a table, and Tony raises a toast to his family, reminding them to savor and enjoy the "little moments."
When Tony is leaving Dr Melfi's office after threatening her life, you can see through the side of the door before it closes that James Gandolfini (Tony Soprano) does not leave, but in fact waits there outside for the next take of the scene.
At 25:23, after Dr. Melfi decides to unlock her door to let Tony into her office, the door drifts open before she manages to insert her key, indicating that the door was neither locked nor closed.
The song playing just after Tony kills Chucky Signore is "It's Bad You Know" by R L Burnside.
The song playing at the end of the episode is "State Trooper" by Bruce Springsteen.