Goren and Eames investigate the murder of a former nurse and discover a possible anthrax terrorist plot. The case takes a turn for the worse when Goren is blamed for driving a suspect to commit suicide. Now disgraced, Goren learns that a cunning adversary from his past may be involved.

Logan and Barek investigate a series of home invasions that result in grisly murders and their search leads them to local foster mother Chesley Watkins who had a series of young men going in and out of her home throughout the years. One of the young men involved in the home invasions was one of her boys, and while trailing the young man, Logan shoots a suspect who was brandishing a weapon at himself and Barek. When the suspect turns out to be a cop, Logan finds himself in the hot seat, and Barek sticks up for her partner, knowing that the truth is on their side. The investigation leads to Watkins as a suspect, and Logan is forced to deal with memories from his own past as Watkins plays on the weaknesses she sees.

Goren and Eames investigate a fire at St. Gerald's which led to the death of a Church employee and soon realize that an arsonist around town is targeting churches. Throughout their investigation, they realize that St. Gerald's was the arsonist's primary target, and clues lead them to Justin Reid, who had donated $100,000 to rebuild the Church, his step-mother Regina, whom they soon learn had seduced Justin when he was only a teen, and his half-brother Glynn, who works for a clean-up crew that had worked at all the churches that were burned down shortly after they were renovated. Deakins comes under fire when an e-mail surfaces that insinuates he got Martinez (from To the Bone) to lie about the Logan shooting by getting him a promotion. The e-mail is soon traced back to former cop Frank Adair (from Season 4, Ep. 22 - My Good Name), who is doing time for murder.