A young teenage girl goes missing from near her bus stop before school. Her exclusive friendship with another girl gives the team a lot of information about the person, but not a lot about where she is. When her distraught best friend goes missing shortly afterward, the team seriously suspects paedophilia-related abductions and has the difficult task of finding both girls.
Flight attendant Linda Schmidt goes missing after leaving her apartment, supposedly heading to the airport to catch a late flight. Evidence found in her abandoned car suggests she may have fallen victim to a serial killer, but all is not as it seems.
Audrey Rose-Beckworth disappears on her wedding day. Evidence suggests that she has been abducted, but the team uncover a past tainted with drug abuse, and a one night stand prior to her wedding day. Somehow, everything relates to the groom's family, which whom she has a close connection, but the secrets run deep and family members are reluctant to reveal them.
Clare, a mentally unstable teenage girl, goes missing from the institution where she is being held. She had been living with her father after the death of her mother. The team must delve deep into her past so that Danny can work out where she is, and rescue her before it's too late.
Bull Carver goes missing after a party held to mark his return to civilian life after retiring from the army. A grudge between Bull and his army buddies that goes back to a time when they were serving together abroad may be the cause of the missing man vanishing. Jack and his team must juggle the concept of military justice with their obligation to uncover the truth.
A well-liked teacher who is eager to change the world disappears after teaching late at the high school where he works. As the team investigates, they soon discover he may have over-stepped his boundaries with a few of his students.
A boxer vanishes moments before a fight that would've meant a big payout had he won. The team uncover a shady family background and a history of match-fixing involving the boxer's brother. Several people connected with the boxer seem to know more than they are telling.
Jack finds himself at the center of an investigation into how missing persons cases have been handled, including such controversial cases as that of Graham Spaulding (recurring guest star CONOR O'FARRELL), the accused pedophile now on trial whose confession Jack may have coerced. As each squad member is interrogated by a representative from the Office of Professional Responsibility, a level of paranoia and distrust is established among them, leaving all of their professional futures in question.
In part one of a two-part season finale, Jack and his team search for an office worker, Sydney Harrison (recurring guest star MARSHA DIETLEIN BENNET), who disappeared from her building. Within hours of Sydney going missing, her employers receive a ransom note via e-mail demanding $50,000. Part 1 of 2
In part two of a two-part season finale, Jack's squad must determine the best course of action when Samantha is shot and possibly critically injured in a hostage situation. After the ransom drop for a woman who has disappeared goes dreadfully wrong, Samantha becomes trapped in a bookstore by the kidnapper, Barry Mashburn (recurring guest star TOM IRWIN), who has discovered that she is an FBI agent. Part 2 of 2
A bus full of students goes missing during the middle of its morning round. It becomes clear that the bus was hijacked. When it is finally located, it is empty save for one student who explains that the hijackers were two of his classmates who want a large ransom.
A priest from a poor area of town goes missing after a car accident in the city. He needs to be found quickly because he is in need of a liver transplant, and a donor liver has just become available but can't wait for long.
A high school boy goes missing. His family, when interviewed, has no idea where he is and he does not seem like a runaway. When interviewing his friends, the team uncovers information about very wild parties that the students have been having, and suspect the boy's disappearance may have had something to do with an event at one of these parties.
An unknown boy is seen being kidnapped and placed into an SUV in a neighborhood with a large population of undocumented immigrants. Despite no missing person report by the boy's family, the team is able to identify him as a local kid who, for one reason or another, had been desperately trying to get his hands on some money by exchanging cans and selling some of his belongings.
A fire-fighter goes missing, just after a large fire in which one of his close friends, despite having been saved from death, ends up badly injured. Although he had told his wife he was heading home, the fire-fighter disappears on the way.