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 an 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.

After Jimmy and Pussy are arrested in an FBI raid, Makazian tells a stunned Tony that Pussy may be wired for the Feds. Tony sends Paulie to find out for sure. Later, Tony learns that Makazian might be trying to frame Pussy to get out of his gambling debts.

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.

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.

Tony's concerns that his mother will rat him out to the feds expire when she, literally, does. Later, Janice arrives to arrange the funeral, which takes a bizarre turn.

Christopher finds that being a 'made' man isn't all it's cracked up to be. Meanwhile, Janice moves into her mother's house, where she soon gets a leg up on Livia's former housekeeper.

A somnolent visit with the ghosts of Christmas past lands Tony back on Melfi's couch. With the annual pork-store holiday party approaching, Bacala reluctantly agrees to don the Santa suit that Pussy used to wear. Tony and Furio have a holiday surprise in store for the Russian who roughed up Janice.

With Paulie in jail, Christopher becomes acting capo, but he gets off to a bad start with Patsy. Still troubled by Jackie Jr.'s death, Meadow contemplates taking a year off from college to travel. Meanwhile, Adriana is in a bind after ending her friendship with Daniele, and Silvio discusses a misunderstanding at a Newark riverfront construction site.

Tony sizes up a contractor's gift, then reunites with his paroled cousin, Tony Blundetto. Paulie and Christopher relive some not-so-special memories. Carmela launches a film club. Adriana grapples with her guilt. A familiar figure 'crosses over.'

Gene Pontecorvo makes a final break from the mob life, while Junior's paranoid delusions could be the end of Tony.