The FBI's New York Missing Persons Squad consists of the boss, Jack Malone, and his team: Vivian Johnson, Danny Taylor, Samantha Spade. Martin Fitzgerald joins the team at the start of season 1. In addition to working for the FBI, Jack is trying to be a decent father and deal with a separation from his wife. Samantha is overcoming the secret affair she had with Jack, her boss. Martin is adjusting to being the newest member of a well-established team. His father is a Deputy Director for the FBI, which makes Martin worry about receiving special treatment. One of the re-occurring cases is a man named Chet Collins who is desperate to find his son missing for 5 years after a camping trip. Throughout the season, Chet makes appearances with Jack to check and see if any new leads have been found. The team thought they had hit a dead end--until Chet himself goes missing.

As the team continues to track down missing people, Jack and his wife slide towards divorce, while Jack must also care for his father (Martin Landau) who has Alzheimer's disease. We learn more about the team members' life histories, including the fact that Martin was practically raised by his aunt and uncle, and Danny is an orphan whose brother (Alex Fernandez) is a convicted felon. Martin fatally shoots a man whom he provoked, and both he and Vivian must keep quiet in order to keep their jobs. Jack makes a last ditch attempt to save his marriage by moving to Chicago with his family, giving Vivian a long-awaited promotion to his post, but at the last minute his wife leaves without him, taking their daughters with her.

Vivian loses her promotion when Jack returns to his job, causing some friction among the group. She also experiences heart trouble that endangers her life and her career, and undergoes risky surgery. Martin and Samantha begin a secret office romance, but it ends badly. Jack undergoes a brutal custody battle with his ex-wife. Danny has to confront his traumatic past and his estranged brother. The season ends with a cliffhanger as a hired mercenary opens fire on Martin and Danny's car while they transport a prisoner.

After barely surviving the gun battle that ended Season Three, Martin must recover from near-fatal gunshot wounds while Danny battles PTSD. Stretched for help, the team gets a new member, Elena Delgado, a former NYPD vice squad officer with an aggressive, streetwise attitude. She has a past connection to Danny, the nature of which is unknown until Season Five. Martin develops an addiction to painkillers, and Jack begins a romance with the widow of a former mentor killed in the line of duty.

Jack's girlfriend miscarries and abruptly ends their relationship. Danny and Elena begin to date each other, while her ex-husband, Carlos, sues for custody of their daughter, Sofia, and later abducts the child. More about Samantha's difficult past is revealed, including her strained relationships with her mother and sister. Jack is abducted and tortured by a psychotic woman, but initially appears to show few effects. At the end of the season, Carlos is freed, leaving the team worried about Elena's safety, and a serial kidnapper appears to be preying on young women.

Vivian is put in charge of a task force to locate the serial kidnapper, who is part of a sex trafficking ring. Samantha reveals that she is pregnant from a one-night stand with a bartender, Brian; by the end of the season, he waives paternal rights and she gives birth to a son. Jack begins a pattern of roughing up suspects to make them talk, which appears to be related to PTSD. He also gets into a dangerous situation without backup and is nearly killed, and becomes over-involved in the life of a teenager he saved from the sex traffickers. In the season finale he is demoted and put in mandatory therapy with Dr. Clare Bryson (Linda Hunt).

This season also contained a two-part crossover episode with C.S.I., as Jack and Gil Grissom and their teams track down a serial killer responsible for the disappearance of a boy six years ago.

The series' seventh season began airing September 23, 2008 on a new 10:00 p.m. (EST) Tuesday timeslot. Steven Weber joined the cast for the first five episodes of the season as Special Agent Clark Medina, Jack's temporary replacement as unit supervisor. The episodes focused as much on missing persons cases as Medina's war against Jack, as he revealed that he had not only been sent to replace Jack but also to convince him to leave the bureau. Medina ultimately realizes that he cannot get Jack to resign, and uses him in a power play to get himself promoted; in return, he arranges for Jack to get his old position back. Following Jack's return to Unit Supervisor, he sets about trying to repair his relationship with Sam and takes custody of his elder daughter, Hannah.