A young successful marketing executive goes missing. Although her life seems full of happiness and achievement on the outside, the team learns she is actually living a sad and lonely life full of drugs, family issues, and failed relationships. Martin has a serious lapse in judgment on his first day on the job.
A young boy goes missing from the subway, after he was separated from his father by the crowd. As it was his birthday he was being taken to see a baseball game as a present. Although his friends claim to have seen him after his father did, and say he scalped his ticket, there is still no sign of him.
Emily Muller is kidnapped while shopping at the mall with her husband. The team discovers that all is not well in her marriage and that her husband may be hiding crucial details that could help find her.
Aspiring model Eve Cleary goes missing but the team have trouble finding people who really knew her. During the course of the investigation, they discover that she has really gone missing twice, under two different identities.
Andy Deaver, a student at the Spaulding Academy boarding school, goes missing after telling his mother he wanted to leave the school for good. Suspiscion instantly falls on head teacher Graham Spaulding, but the team have trouble pinning anything on him. Jack is forced to break the rules in a desperate attempt to save Andy's life.
Patrick Kent, vice-president of a huge New York company owned by his father-in-law, disappears in an airport in San Diego. He is apparently intending to fly home to New York from a business trip he took on a regular basis, but the team uncover a secret life which may suggest that he never intended to return to his old one.
Abby Buckman, the toddler daughter of an assistant district attorney, goes missing while in the park with her nanny. The team investigate every aspect of her parent's lives in a bid to uncover a motive for the disappearance, but they keep hitting a brick wall. After a red herring ransom call, they discover evidence that suggests Abby may not have been the real target of the kidnapper.
A teenage boy who lives in foster care goes missing from his work in a diner. His siblings are in different places around the city. Although all reports say he is a good, hard-working kid, the team has to suspect some sort of illegal activities or gang problems.
Dr. Anwar Samir, a third year resident at a New York hospital suddenly goes missing following a disagreement with his superior and the rejection of a proposal by his girlfriend. Given his Saudi Arabian background, almost inevitably suspicions arise of terrorist links. Witnesses and colleagues begin to question past "suspicious" behaviour, and disagreement manifests within the team itself as to the presumption of guilt as the Joint Terrorism Task Force also becomes increasingly involved.
A father and his young daughter go missing on the way to school. While initially suspecting that the father has been having an affair, when the team digs further into his background, they discover nothing is what it seems with this man. His true identity and the reason behind the disappearance is not revealed until they locate his daughter.
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, 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.
Jack and his team search for an office worker, Sydney Harrison, who disappeared from her building. Within hours of Sydney going missing, her employers receive a ransom note via e-mail demanding $50,000.
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, who has discovered that she is an FBI agent.