FBI profiler Gideon begins to doubt his abilities and sanity in the aftermath of the murder of his girlfriend at the end of last season and ultimately leaves the BAU. The team is confronted with cases involving all manner of killers, including one cannibal. Derek must confront his crisis of faith. In another episode, Reid attends a support group for his addiction. Two cases hit close to home. In one, a team member is shot, and in the explosive season finale, another is targeted by terrorists.
A spree killer has committed multiple murders of brunette coeds at a college campus when the BAU is assigned to the case. The murders are taking place in plain sight, with no fighting back from the victims. This leads the unit to believe the killer is a part of daily life on campus; someone who would put a victim at ease.
In Milwaukee, a series of women have been found murdered with their hearts crudely removed. The BAU is assigned to the case, but they are short three members: Gideon, who is missing, Hotch, who is on suspension and Prentiss, who resigns her commission to join the Foreign Service. Supervisor Strauss steps in as lead, but she doesn't handle herself well in the field.
The team investigates a group of bodies discovered buried in various states of decomposition in Portland, Oregon. The mode of death varies dramatically, which is unusual since most killers have one MO. Soon a new disappearance comes to their attention, and it becomes clear that they are working against time.
The BAU is called into help the local authorities in Cherry Creek, Colorado after a series of brutal home invasion murders. Quickly the team recognizes two different signatures, fitting two distinct personalities. The first man kills the parents violently, while the other drugs the children like an "angel of mercy" murderer. But the two men come under a microscope when one of their victims survives an attack. The girl, Carrie, now an orphan, says the men call each other "brother," despite the fact that they are of different races.
When a local girl named Katie is kidnapped in the Potomac Mills mall only weeks after another child is kidnapped and murdered in a similar kidnapping, the BAU moves in. The mall is locked down while the FBI searches the stores, but it's a painstaking process. The parents are hysterical, while the girl's cousin, Jeremy, has a panic attack as he tries to remember the last time he saw Katie.
A new member joins the BAU, but he's a familiar face to some of the team: David Rossi. He was one of the founding members of the unit, but he took early retirement and became a famous author. Now, Rossi's "unfinished business" has led him back to the job, and he's even willing to accept a subordinate position.
The BAU is called in to Montana when a woman is kidnapped from a grocery store by a member of an anti-government militia, Francis Goehring. When he's cornered by police, he blows himself up with a grenade when he's cornered by police, but the woman is nowhere to be found. After digging into Goehring's past, they find his former wife, who points them to a location where it's likely the kidnap victim was taken. There they find her dead body, skin still warm. Goehring didn't commit the recent murder; he has a partner who's still alive. But he did commit three earlier murders, and Prentiss finds each of them buried in a rose garden.
When a homicidal Satanist commits an extremely violent murder in Florida, the team flies in to take the case. The religious angle stirs up memories in Morgan, who has been away from the church for years. Soon Hotch learns that the murder is only one of a long line of killings, which undoubtedly means there will be more to come.
Garcia has been shot, but still alive on the stoop of her building. Though Garcia's heart stops on the table, she pulls through. She answers what questions she can about her date, but the results don't lead anywhere. Meanwhile, her "date," James Colby Baylor actually shows up at the scene the following day, stunned to find out she survived.
The team arrives in Los Angeles to cover the crimes of a serial killer in the midst of a psychotic break. Multiple brutal murders have occurred in a two week span, and the team focuses on a three block radius surrounding the scenes. Soon, six gang-bangers turn up dead in a nearby neighborhood, with the gang leader missing. The MO is the same as the other murders, which means the killer has ventured out of his territory for a reason.
When a series of women go missing in Fredericksburg, Virgina, the team takes the case. Jareau is having a tough time with this one, since most of the victims, burned and mutilated, are women around her age. Soon Garcia turns up evidence of another series of killings that took place in the same town in the 80s, identifying one woman who survived. Karen Fowler escaped her attacker, but she refuses to help the BAU.
When one teenager is found murdered and her best friend is abducted in Chula Vista, California, the BAU must profile the killer and find him before he kills the other teen.
An auction for the contents of self-storage facility in Philadelphia uncovers a roomful of items that might be indicators of a serial killer in the making. Rossi and Reid head up to investigate, and the items sway Rossi into believing they have a killer on their hands. As the team dissects the history of their UNSUB, they find a victim from four years prior matching the signature of the killer. Three more bodies turn up, but they believe the killer has become better at hiding his victims over the years.
Rossi goes to Indianapolis to continue his investigation into the two unsolved murders that have plagued him for 20 years, and he is joined by Prentiss, JJ, and Morgan when they learn about the case. Meanwhile, Hotchner and Reid interview a death-row inmate in a Connecticut prison.
The BAU is called to Pittsburgh after an unusually high suicide rate appears to be the work of an Angel of Death.
The BAU is called to West Bune, a small town in Texas, to investigate what appears to be spree killings that involve a teenaged boy and his girlfriend.
The BAU is called to Miami to investigate a serial killer who appears to have a conflicted sexual identity. Meanwhile, JJ's secret is revealed.
The team members try to identify a stalker before he can attack a woman who is being stalked in Silver Spring, Maryland.
After a suspected serial killer wakes up from a coma, the BAU reopens the case and uses brain fingerprinting to determine if he really doesn't remember the crimes that had been committed four years earlier in Roanoke, Virginia.
The BAU faces one of its toughest cases when the team is called to New York City to determine if a series of random shootings is the work of one serial killer or a team of killers working together.