The second season of Criminal Minds premiered on CBS on September 20, 2006 and ended May 16, 2007. Lola Glaudini left the show after six episodes, and was replaced by Paget Brewster two episodes later.
Having been a guest star for Season 1, Kirsten Vangsness was finally promoted to series regular, coming last in the opening titles after A. J. Cook.
The BAU team continues to unravel the clues given to each of them by a psychopath in order to save his most recent victim. Gideon decides not to focus on the personal aspects of the case. Rather, he tells the team to profile the killer as they would in any other investigation. Reid stays behind to work on a personal connection that could solve the case as one member of the team fights for life.
A young boy who had disappeared a year ago turns up for for sale by a child pornographer on an online auction. A former profiler who now heads the FBI's Innocent Images Unit asks Gideon and the BAU to help her save the boy's life.
The BAU has reason to believe a series of murders might have been committed by two people working as a team after the victims' families receive DVDs after each crime that includes psychological attacks.
The BAU is called to investigate a series of bank robberies after it becomes evident the crimes are not based on money because the robber abuses his victims by forcing them to undress before he leaves the crime scene.
The BAU investigates a serial rapist who had been attacking young women at religious schools and stopped for six weeks. He has resumed his attacks, but is now targeting a different demographic of women. Elle makes a decision that could end her career with the BAU.
The BAU travels to a small Texas community to investigate the murders of children. Meanwhile, Elle is having readjustment issues after being shot, and Hotch becomes worried about her when she misses a mandatory psych evaluation and isn't answering her cell phone.
After a man kidnaps three teenaged girls and locks them in a cellar, he tells them only two of them will live and they must choose which one will die. The BAU team takes the case when the mother of one of the girls travels to Quantico to ask JJ to intercede with the FBI on the girls' behalf.
The BAU travels to Seattle to identify and catch a serial bomber who has been terrorizing the city and targeting centers of automated techology. Working with the author of a science fiction novel that has become a guide for the bomber, the team attempts to determine why certain sites have been chosen as targets.
The daughter of high-powered diplomats, Special Agent Emily Prentiss joins the team, and she must convince Gideon and Hotchner she deserves the job based on merit and not on her family connections. The BAU is then called to St. Louis to investigate two serial killers who appear to be competing with each other. By setting a trap based on one killer's profile, the team creates a media event by which to capture the second killer.
Gideon, Reid and Prentiss travel to Guantanamo Bay to interrogate the leader of a terror sleeper cell being detained there after a chemical weapons dispersal device is discovered during a raid at a suspicious house. Working with Reid, Emily's fluency in Arabic proves to be useful as they scrutinize the suspect.
The BAU is called to investigate the serial murders of prostitutes in Washington, D.C., and suspect a teenager is guilty of the crimes. The case becomes complicated when a congresswoman about to make a speech to praise the city's lower crime rate threatens to take away the case if Hotch calls a press conference to discuss it.
Morgan is arrested as a serial killer after he goes home to Chicago to visit his family. Because the detective making the arrest had used a profile provided by Gideon, the team travels to Chicago to help the local authorities find the real killer and exonerate Morgan.
Gideon is pitted against the scariest and most evil murderer in his entire career. When the BAU confronts the sadistic killer in a remote diner in the Nevada desert, the local authorities want to move quickly and make an arrest. But Gideon bides his time as he attempts to persuade the man, who has sworn not be captured, to reveal the whereabouts of a woman he is holding hostage.
In this special two-part episode, the BAU is called to investigate after a wealthy couple is murdered in their home following a Super Bowl party. The team pursues what they believe might be multiple killers who use webcams to record murders and upload the tapes on the internet. Hotchner, Morgan and Prentiss soon discover the unsub is actually one man with multiple personalities. As they close in on the killer, Reid faces a life-threatening situation.
In this conclusion of a special two-part episode, finding the serial killer becomes critical to the BAU when the team realizes Reid is being held captive and a live feed of him being tortured is shown on the internet. Meanwhile, Reid's troubled childhood is revealed in flashback sequences as he drifts in and out of consciousness.
The BAU becomes involved to prevent a possible race riot when the murder of four young black women in a mostly white New York suburb appear to be hate crimes.
The BAU travels to Houston to investigate a series of murders that have occurred near construction sites and abandoned buildings. Because the murders appear to be random, the team believes the killer could be a homeless person. Meanwhile, everyone is noticing an apparent change in Reid's behavior.
A case involving a serial killer believed to be copying Jack the Ripper takes Gideon to New Orleans after three victims are found with their throats cut. Once thought to have been killed in Hurricane Katrina, the discovery of a fourth victim in the French Quarter confirms the murderer is still alive. All the evidence and files had been lost in the flood, so the only clue the team has is the word "Jones" that the lead detective wrote on the wall just before he drowned. Meanwhile, Reid meets up with an old rival as he continues to struggle with the aftermath of being held hostage.
A serial arsonist who targets the homes of upper-middle-class families as they sleep is investigated. The BAU determines the arson victims are linked together through corporate development companies that have been accused of building on contaminated land.
Elizabeth Prentiss, a foreign ambassador and SSA Emily Prentiss' mother, seeks the aid of the BAU when a Russian immigrant is kidnapped and held for ransom.
The BAU is called to investigate after the bodies of missing people are discovered in a remote region of the Idaho wilderness. The gruesome find also leads the team to determine the unsubs have been hunting humans for sport.
When homeless persons begin going missing mysteriously from the streets in Kansas City, a local detective calls the BAU to investigate the disappearances.
When the prolific serial killer Frank returns and murders Gideon's girlfriend, Gideon takes off to find him without telling the team where he is going. The BAU must then profile Gideon as well as Frank to find both of them.