Just days after Sylvia gives birth to a baby boy (Theo), Sipowicz suffers an emotional setback when Andy Jr. is found murdered in the line of duty. Sipowicz wants Simone to lead the case of his son's killer and also wants the opportunity for restitution. With Russell in tow, Simone tries to balance his desire for revenge, as well as his quest for justice to catch the killers. While Sipowicz breaks the news of his son's death to his first wife, Katie, he begins to show signs of an emotional breakdown. In the midst of all this turmoil, Donna makes her decision when she quits her job as administrative assistant to the precinct and moves to California, leaving New York for good.

Simone and Sipowicz investigate a crime where a man discovers a woman's body stuffed inside a large box. While on the case, they meet the victim's brother, a strange man who is more concerned with drinking a particular brand of soft drink. Meanwhile, Russell investigates the death of a child whose parents do not seem fit to raise a child. Also, Kirkendall and Medavoy look into the death of a young boy whose very religious parents suggest that the person who killed their son can be forgiven.