Lilly re-investigates the case of a murdered church organist (John Walcutt), when his Alzheimer's-stricken widow (Isabella Hofmann) begins having flashbacks of the night in question. Lilly's investigation has both Mitchell's son, Ryan (Jimmi Simpson), and daughter, Tina (Daisy McCrackin), demanding Lilly close the search.

A petty crook, Ricky (Tim deZarn), hoping to get a reduced sentence, relates witnessing a young man washing blood out of his car the night a teen track runner was murdered. The young athlete, Paige Pratt (Summer Glau), was found shot, and her boyfriend Al Clarkson (Doug Kruse) was originally imprisoned for the crime.

Lilly investigates an unsolved hit-and-run accident from New Year's Eve 1999 that left a man dead, after a recovering alcoholic comes forward and claims she is the one who hit him. But the evidence points to the guy being murdered, not accidentally run down.

Lilly reopens a 1990 murder case, in which a prep-school girl was found dead in a local swimming hole, after a present-day victim with similar markings is discovered at the same place. The investigation reveals that the victim of the earlier crime was routinely tormented by a trio of classmates who invited her to a sleepover the night she was killed.

The team re-opens the 2000 case of a prominent Puerto Rican assistant district attorney when rumors about his connection to a large amount of money gone missing at the time of his death start to circulate. However, his widow insists that the claims are not true. The re-investigation reveals that the victim was prosecuting a murder trial and the man convicted for the crime after his death may possibly be innocent.