Lilly returns to her last case before joining the Cold Case Squad as she re-investigates the brutal triple homicide of a restaurant owner and his family, murdered in the restaurant bathroom in 2003. Also the other team member have personal reasons to closing the case; Jeffries grew up in the predominantly black neighborhood while Vera was the one assigned to the case when Det. Rush left.

On the eve of the 60-year reunion of women who worked in a weapons factory during World War II, Lilly is asked to re-investigate the death of Alice Miller, one of the worker girls. The death was deemed accidental at the time, but her friend pleads to Lilly to look closer into the case.

Lilly and Valens reopen a presumed homicide from 1979 in which an unidentified victim's blood-drenched shoes, underwear and sheets were found in a trash bag, but no body. The investigation begins when a battered wife accuses her husband of murdering a girl in 1979 and brings in an amateur film from the time that supposedly shows him committing the crime.

When human remains are found outside a former state prison, the team re-opens the 1968 case of a dead inmate, murdered on the night Johnny Cash's Folsom Prison Concert was broadcast to prisons throughout the country. However, when it's revealed that the bones don't belong to the person everyone had assumed, the team must start the probe anew by first identifying who the victim was.

Det. Rush investigates the 1991 double murder of married illegal immigrants from Cambodia who were shot to death in their apartment and found by their 6-year old daughter. The now-teenage girl brings the case to Lilly after she discovers a bracelet once owned by her mother is for sale on the internet. The probe reveals that the parents had dark secrets unknown to their daughter.

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.

An HIV-positive gay man asks Rush and Valens to re-investigate the case of his dead partner who died of strangulation in 1983. Not only was the victim outspoken in his views about AIDS education within the 1980's secretive gay community, he was also the member of a very prominent family, disowned by his father for his sexual orientation.

The 1953 murder of a white school teacher, a communist sympathizer who was involved in civil-rights issues, is reopened after the victim's youngest son asks for it to be reinvestigated. The probe reveals that the slain man was killed on the same day that the Rosenbergs were executed and was set to testify the next day before the House Committee on Un-American Activities.

The headless torso of a woman who disappeared in 1985, on the same day she filed domestic-abuse charges against her husband, is found by hikers in a wildlife preserve. The investigation quickly leads to the grisly discovery of 8 more decapitated bodies, the victims of a serial killer.

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.

The team re-opens the case of Matthew Adams, a teen-aged cult member who apparently committed suicide back in 1978, when his sister comes forth with new evidence about the deprogrammer her family hired to rescue her brother.

When a dying boxing referee makes a confession about a 1976 fight, the team re-opens the case in which an underdog fighter, arranged to fight against a much more qualified boxer, took a heavy beating in the match and died only moments afterwards.

After a murder weapon connected to the 1987 drive-by shooting of a little girl turns up, Det. Rush and her team re-open the case. The team slowly tracks back the gun's previous owners until the shocking original owner is finally revealed.

Lilly investigates the 1993 death of a mentally challenged teen who was hit by a train, after drawings appear on his grave that indicate foul play might have been involved.

Lt. Stillman's priest informs him of a long ago confession where a man confessed being involved in the 1998 kidnapping of a 9-year old boy. The case is reopened with this new lead, and it turns out the truth is closer to home.

A man claims that he was wrongfully convicted of the 1982 murder of his rich wife. The case is reopened when the victim's rare ring is discovered worn by a recently deceased junkie.

A woman, who was romantically involved with Nick Vera in high school, claims that members of a fraternity might have been involved in her alcoholic sister's death in 1995. The victim's estranged husband and a bar owner are also viewed as potential suspects.

The unsolved 1963 murder of a black teenager, whose body was discovered by the then-young Will Jeffries, is reopened.

The murder case of a young mill worker is re-opened when Rush learns that a recent parolee admitted to stealing money off the victim's body.

A convicted serial killer will be paroled after 25 years in prison unless Lilly and her team can connect him to the 1977 murder of a young doorman found strangled on a train platform. The killing is eerily similar to other murders committed by the man. Making the case more urgent is the fact that the convicted strangler hints that he will kill again upon release. Elsewhere, Scotty confronts Christina about her past and tries to get her to talk to a New York detective.

When an old truck containing human bones is pulled from the Delaware River, the team re-opens the case of a missing and possibly murdered girl who disappeared unexpectedly in 1932.

The discovery of nine human skulls leads Rush (Kathryn Morris) back to George Marks, the serial killer she was unable to incriminate months earlier, and who walked away a free man. As the detectives reinvestigate his mother's murder from 1972, George is forced to emerge from hiding to face Rush again. This time, their very lives are at stake in their final showdown.