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.
At Tony's suggestion, Junior is made acting boss after Jackie dies. In therapy, Tony surprises Dr. Melfi with a surprise admission. Carmela and Irina (Tony's mistress) both suffer as Tony's libido takes a nosedive.
At the wedding of Larry Boy's daughter, the 'boys' find out they're going to be indicted, and make a premature exit to get rid of incriminating evidence at home. Upset that he isn't getting the notoriety of other family members, an agitated Christopher has an ugly encounter with a bakery clerk.
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.
In the Season One finale, Tony is stunned to discover that the attempt on his life may have been ordered by someone very close to him. Later, he must deal with the fact that everyone knows he is seeing a shrink. Christopher is sent to take care of Jimmy Altieri.