Lilly investigates a 1995 shooting spree at a mall in which two teen boys killed 15 people before committing suicide. The case is reopened when a video of the crimes is found and it suggests that a third shooter was involved. Elsewhere, Stillman asks Valens to investigate whether Valens' brother may have been molested by a boxing coach in the 1980s.

A 2004 case in which an Iraq War veteran abruptly disappeared is reopened after the missing woman's prosthetic arm is found in the Delaware River.

The 1948 death of a miner is investigated after transit workers find his body in a service tunnel five stories below a river while expanding the subway system. The deceased was also a married white man in love with a widowed black woman. Also, Lilly feels uncomfortable when Joseph tells her that he loves her.

A 6-month-old girl's 1982 death, originally ruled to be a result of sudden-infant-death syndrome, is investigated when new evidence reveals the baby may have drowned. Also, Lilly learns that Ray is in the hospital after apparently being beaten.

The parents of an autistic boy are gunned down in their car while on their way to get takeout. The 2003 case is reopened when Joseph informs Lilly that the boy, now in a state institution, blurts out a specific number whenever the parents are mentioned. It's soon learned the boy was in the car when the murders occurred, but he's unable to identify the killer. In a more personal matter, Ray tells Lilly he's leaving for California and wants her to come with him.

The apparent 1958 suicide of a popular rock-and-roll DJ is reinvestigated after a documentary filmmaker discovers a tape recording made at the time of the victim's death by gunshot at his radio station. Also, Valens tries to get his brother to testify against a suspected pedophile.

The 1979 murder of a schoolteacher who was stabbed to death in a wooded area is reopened when the victim's bloodstained jacket is found stuffed in a tree trunk with a happy-face key chain in a pocket. The case was originally investigated by Jeffries when he was a rookie detective.

The 1975 disappearance of an 8-year-old girl who was never found is reinvestigated after a note written by the girl shortly before she vanished turns up. Their friendship rattled many in the predominantly white neighborhood and the girls quickly became targets of hatred.

A homely 33-year-old woman is gunned down in an alley in 1989 and her unsolved murder is reinvestigated when a tape of the victim, made for a dating service, turns up in a suicide victim's apartment. Apparently, it was what the man was watching when he killed himself. Also, Vera moves into an apartment of his own

The unsolved 1968 murder of a policeman is reinvestigated when a dying inmate claims he took a brick of heroin from the slain officer's patrol car shortly after the victim was gunned down in the same vehicle. but new evidence now reveals the victim may have been romantically involved with his partner.

Lilly and Valens travel to Nashville and Knoxville to investigate the 2000 murder of a country-music singer who was gunned down outside of a Philadelphia bar where he and his band had recently played. The unsolved case is reopened when the gun used in the homicide turns up.

Lilly investigates the murder of a 17-year-old prep-school student who disappeared in early 2006 and whose body is found stuffed in an oil drum outside an abandoned warehouse in a drug-infested part of the city. Also, Vera pays a parking ticket for his neighbor and later asks her out on a date.

Lilly investigates the 1996 murder of a wealthy divorced woman who was found dead in her ex-husband's indoor swimming pool. The original investigation ruled the death accidental, but new evidence suggests it was a homicide.

Two teens, one a preppy 13-year-old Chestnut Hill girl, the other a 15-year-old North Philadelphia boy who is a drug dealer, are both shot to death on the same January day in 2002 at 8:03 A.M., outside of different schools. The cold cases haunt Miller because it's the fifth anniversary of the shootings and she was the one who found the dying boy. She believes the cases are connected, but Lilly doubts that they are related.

Lilly investigates the deaths of a married couple who perished in 1981 when a supposedly accidental gas-leak explosion set their house on fire. The case is reopened when fragments of a bomb are discovered at the house during renovations. Back at headquarters, Stillman takes care of his 4-year-old grandson.

LLilly investigates the 1964 murder of a 17-year-old girl who was sent by her parents to a home for unwed mothers, where she gave birth to a girl. The next day the teen was killed. The case is reopened when the victim's daughter comes forward, having just learned that she was adopted and that her biological mother was slain.

When a body is found in a dumpster, the team re-opens the 1984 case of a murdered teenage boy who wanted to become a dancer against his father's wishes.

The 1999 murder of a homeless woman, whose body is found at the bottom of a river in a station wagon, is investigated.

A father pushes a registered sex offender off of a building and threatens to kill a different sex offender each day until the cold-case unit solves his son's 1987 rape and murder.

The 1997 murder of a 16-year-old girl high-school cheerleader is investigated after an anonymous confession is discovered in a modern-art exhibit.

The team re-investigates their oldest cold case yet, the 1919 murder of a young woman who was a passionate advocate for women's right to vote.

The 2005 murder of a longshoreman who accidentally became involved in a human-trafficking ring run by the Russian mob

The 1998 death of a terminally ill man who died months before he was expected to is investigated after a nurse confesses to six so-called mercy killings.

In the fourth season finale, a hostage situation arises when the entire team is held captive while they're investigating the 2006 killings of a family who had just moved into a new house.