Marcellus gets a new partner, Aldo Rossi, and Mike has trouble adjusting to the change; after initially resisting Heather's suggestion that he reconcile with his father on his upcoming birthday, Mike finally relents, but his father rejects both his present and Mike; the ""Inquirer"" reporter who wrote the story of Mike's arrest now wants to paint him as a hero, much to Mike's disgust; when his friend Doug is killed in a hit-and-run accident after he gets out of his cab, Mike promises Doug's son Bobby that he will find the man who killed his father; after finding out that Doug had uncovered a fraudulent scheme at his company, Mike suspects that the company's chief financial officer had a hand in his death, and has mixed feelings when he is proved wrong by Rossi, who uncovers the real culprit.

Mike Jr. is upset when he sees a copy of his parents' divorce decree and gets into the sacramental wine at St. Vincent's, leading Mike to realize the importance of spending more time with his son; Grizz's high school sweetheart comes back into his life when she divorces her husband and comes to work at the parish; the cop who arrested Mike is mounting a case against Marcellus and asks Mike to flip on his former partner; when the cop's son is murdered during a robbery, Marcellus is assigned the case, which goes cold when the only witness is murdered; Mike and Marcellus join forces to find the cop before he administers some street justice to his son's killer; Marcellus offers to help his nemesis cover up his execution of the killer, but the cop declines and turns himself in, giving Marcellus a chance to get out from under his corrupt behavior.

An exhausted E.R. doctor's error results in a man's death, and an upset Heather seeks Mike's help when the hospital administration refuses to take action after she reveals that the doctor falsified the man's chart to cover up his mistake; Mike convinces a reluctant Heather to give the story to reporter Emily Carson, whose investigation results in Heather's being fired and blacklisted on a trumped-up charge; Mike's concern that Heather may have to move far from Philadelphia with Mikey to find work puts a strain on his budding relationship with Faith, who begins to doubt that Mike is over Heather; Mike enlists the help of Ryan Ambrose, a psychiatrist at the hospital who supports Heather, in obtaining information that convinces the E.R. doctor to back up Heather's account of the patient's death and to admit his mistakes to Emily; Heather is reinstated, and she and Mike realize that it's over after spending the night together, leaving Mike free to commit himself to a relationship with Fait

After Mike convinces Marcellus to help him work to free a man they incorrectly helped send to prison, he incurs the further wrath of his father; Mike has mixed feelings when he discovers that Heather is seriously dating Ryan, who begins to provide Mikey with perks that are way out of Mike's league; Grizz assures Mike of his son's love, and Mikey confirms that for his father.

After Bill Olshansky has heart attack which creates irreversible and uncurable heart damage, Mike's decision to take care of his father leads them over rough territory as they hash out old grievances and can't seem to connect; in an attempt to get them to reconcile, Faith provides some words of wisdom for both father and son which finally enables them to bridge the gulf that separates them before Bill dies; picking up on Mike's feelings about Ryan, Mikey begins acting out towards the new man in his mother's life; Grizz is suspended by the bishop after $2,000 is missing from the collection money; Mike enlists the help of Aldo and the altar boys in exposing the real thief; Grizz contemplates leaving the priesthood in the face of his growing attraction to Beth, coupled with the bishop's lack of confidence and support.

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While Mike identifies the man who shot Marcellus as someone who escaped from a drug dealer take-down long ago, a second attempt on Marcellus's life points to the possibility of two different shooters; forced to hide out from some bad guys, Jamie temporarily moves in with Mike, and Liz teaches him how to be a good neighbor.

While Mike is more than willing to assist Jamie in turning a teenage friend away from prostitution, Liz is much less sympathetic to her plight until Jamie convinces her that the privileged upbringing he and the girl shared is no protection against pain; continuing to mentor Cal, Marcellus strikes a bargain with a loan shark to arrest his competition on the street in exchange for his releasing Cal from his crew; Mike walks on eggshells in the face of Liz's anger; after Liz manages to get Cal out of the shelter and into a foster home, Deborah agrees to let him stay at the Washington house until his foster placement goes through even though things are very much strained between her and Marcellus; Mike, Marcellus and Liz use their individual talents to get Jamie's friend out of the hands of her pimp and into the arms of her parents.