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.

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.

Mike and Marcellus work together to free an innocent man caught up in the nightmare of being falsely accused of terrorism by an F.B.I. agent who runs amok under the cover of the so-called ""Patriot"" Act when bombs go off at the Criminal Justice Center; in a misguided attempt to help, Jaime uses Mike's computer to hack into the F.B.I.'s database, which only leads to landing Mike in custody as well; Mike uses his time in custody to figure out that the bombings might be personal rather than institutional attacks, and gives Jaime the opportunity to redeem himself by having him hack into the PPD's database to find the link between the victims, who ends up being an ex-con out to destroy the people responsible for putting him behind bars; Mike and Marcellus track the bomber down just in time to prevent him from harming the next victim on his list, his probation officer, who turns out to be Mike's neighbor Liz.

A young girl who witnessed a murder seeks Mike's help in helping her evade the corrupt police officer who has been paid off to cover up the crime and silence her; Marcellus takes up residence on Mike's sofa as his marital problems continue.

Mike steps in to help his cousin who's caught a downward spiral of addiction and suicidal urges as he combats post-traumatic stress after serving in Iraq.