The season opens with Mac engaged in a romantic relationship with the new coroner Dr. Peyton Driscoll (Claire Forlani). However, later in the season when Mac tries to keep their relationship a secret, Peyton realizes that Mac may not be ready for a serious commitment.
Mac also comes in contact with his deceased wife's son. Trying to forge a friendship with him, Mac is disappointed when he realizes that the boy wants nothing to do with him.
While Lindsay Monroe and Danny Messer had chemistry, Lindsay's past prevents her from moving forward with the relationship.
When processing a case in which a young girl is murdered, Lindsay abruptly leaves the scene and admits to Stella that years ago her friends were murdered and she was spared. This secret has affected her work and personal relationships.
Hawkes endures a tough season when he suffers the consequences of a professional decision he made years ago when he put a psychopath's brother behind bars for murder. The psychopath Shane Casey (Edward Furlong) returns and frames Hawkes for murder.
When Shane reaches out to Danny who also has brotherly problems, he realizes that his brother was guilty; a shocking discovery that leads Shane to disarm.
Eddie also experiences his fair share of conflict when he realizes that one of his men is a dirty cop.
Stella continues to heal from her near-death experience with ex-boyfriend Frankie Mala at the end of Season Two.
CSI: NY is produced by CBS Paramount Network Television in association with Jerry Bruckheimer Television. Jerry Bruckheimer, Anthony E. Zuiker, Jonathan Littman, Carol Mendelsohn, Ann Donahue, Pam Veasey and Peter Lenkov are executive producers.