The team searches for a missing 5-year-old boy and his abductor when they’re tipped off about the abduction by the kidnapper’s 12-year-old son. At the FBI offices, Bryan remains traumatized after barely escaping his enraged father, Randall, who foiled Bryan’s attempt to sneak the 5-year-old Todd out of the house. Bryan reveals that Randall brought Todd home a week ago, explaining that he was watching Todd for a few days for a friend. While Samantha attempts to get Bryan to disclose more about Randall without pushing him over the edge, the rest of the team searches for Todd and his kidnapper while also trying to uncover Todd’s true identity.

Elena goes undercover as an exotic dancer in an attempt to find a stripper who disappeared from the same club, while Danny goes undercover as one of her customers.The team tries to find Cindy Peterson, a missing wife and mother who recently took the job as a stripper to help pay the family’s mounting debt. Since the club is the common link between Cindy and a recently murdered fellow dancer, Jack decides to assign Elena and Danny to go undercover to get some answers. Meanwhile, Jack and Anne deal with the professional and personal ramifications of her pregnancy.

The investigation soon reveals that, in addition to receiving a call from a man who threatened to kill her for interfering with his life, Jessica was also accosted by a man whose wife died while he was seeking Jessica's help on a 911 line. Additionally, though Jessica didn't report it to the police, the team learns that before she vanished, someone broke into her apartment and killed her dog. Meanwhile, Elena still feels awkward about making out with Danny while they were undercover on a previous case.

The team learns that Malia Norton is a smart model resident who is 13 months into her 18-month sentence for a DUI car accident that killed a classmate and crippled her sisters boyfriend. Upon discovering that the detention centers alarm was rigged, Martin wonders if Malia escaped or was the victim of foul play. As the agents investigate why she was recently manhandled and threatened by other detainees, they also try to locate the man who recently visited Malia at the facility.

When Jack gets the FBI involved in the case of Sadik Marku’s missing mistress, Julia, and their 8-year-old son, Petros, Samantha questions whether Jack is more interested in going after Sadik or finding his son. During the investigation, the team learns that a neighbor saw Julia and a blanketed bundle believed to be Petros thrown into the back seat of a car by a man. Among the many suspects behind the abduction are rival gangs and mafia members, as well as Sadik’s wife.

Aaron's wife, Sherise , says she last saw Aaron the previous morning when he left their Queens, N.Y. motel room for a temporary construction job in New Jersey, after just being let go from his cousin's construction site job. However, the team learns that Aaron, whose truck was found abandoned and burned, actually quit his job and lied about having work in New Jersey. Wondering what else Aaron may have been hiding from his wife, the agents entertain theories of foul play and suicide as well as the possibility that he chose to run away from his mounting financial woes.

Katie’s brother asks for Martin’s assistance because Katie spoke fondly of him when she interned at the FBI when Martin was still working on White-Collar crimes. He and the team soon discover that the priest, who also vanished, was suspected of murder last year when a man died during his exorcism. They also learn that Katie scheduled the exorcism because her mental illness, well managed with medications for many years, is now causing her to feel like she’s being possessed by something dark. Meanwhile, Jack and Anne forge ahead with their plans to buy an apartment together as they prepare for their baby’s birth.

After learning that Alex Stark, a missing 20-something man, lied to his girlfriend of three months about owning a cleaning service, the team wonders how he was living so luxuriously. They soon discover his ties to an illegal poker club and that he emptied his account of $48,000 three days prior to his disappearance. Jack goes undercover as a player at the club and, unbeknownst to his team, is soon at the mercy of Cynthia Neuwirth, a dangerous acquaintance of Alex's who is convinced that Jack was hired to kill her.

The team searches for a social worker who disappears after forcibly removing a 7-year-old girl from the home of her violent father and desperate mother.

The disappearance of a terminally ill woman who was searching for a miracle cure leads Vivian to suspect a pair of con men who had been taking advantage of her.

The team searches for a 17-year-old high school basketball star who vanishes the night he scores the winning basket at a game that secures his team’s position in the state championships.

The team initially thinks that Rawlings may have disappeared because of things going on in his personal life -- the death of his wife and estrangement from his son. However, in the week prior to his disappearance, Rawlings reported a suspicious flight pattern of a Middle-Eastern pilot and he was threatened by someone at his home. Now, the agents try to determine whether the pilot may be involved in retaliating against Rawlings, or if there is a much bigger conspiracy in play.

Barry Rosen disappears after his doctor gives him the sobering news that he'll need to stop eating competitively or he'll die of a heart-attack or stroke, and before hearing the test results that say Barry's post-contest collapse was a result of being poisoned with bleach. As the team begins to question his competitors, they also investigate why Barry attacked his brother with a knife days before the contest. Meanwhile, Danny is conflicted when his friend Carlos, who is Elena's daughter's father, asks Danny to write a letter on his behalf for his upcoming custody hearing with Elena.

An artist, whose paintings are based on photographs she secretly takes of strangers on the street, disappears, and the team suspects that someone who was unhappy with being portrayed in a picture has harmed her.

Jack and the team search for a water plant foreman who disappears hours after his life is threatened by a long-time employee who became enraged when the young foreman laid him off. Asserting his innocence in the missing Jason Turner's disappearance, the newly laid-off Earl Dooley tells the agents that Jason gained many enemies during the recent wide-spread lay-offs at the plant. The team also learns that Jason was trying to reconcile with his former fiance , which leads them to wonder if Jason might have found trouble by getting between his ex-fiance and a possible new man in her life. Meanwhile, Elena continues to have custody-related problems with her daughter's father, Carlos, who is irate at discovering that his old friend Danny is involved with Elena.

When a thug abducts Elena’s daughter from home, Jack quickly dispatches Danny and Martin to find her; the team searches for a missing female tourist.

As the team searches for a missing U.S. Senator, they are forced to contend with her powerful and meddlesome father and the media that is tracking the case.

The team searches for a teenage girl last seen being followed out of an internet cafe by a male teen who just passed her a lewd note. Samantha's estranged sister attempts to reconnect with her.

Samantha secretly attempts to search for her missing sister with the aid of just the local police until Jack learns about her sister’s abduction and insists that their team get involved.

When the 6-year-old boy of an interracial couple is kidnapped while out with his momentarily distracted mother, the team wonders if the boy’s estranged wealthy white-supremacist paternal grandfather could be connected to the abduction.

When the team begins their search for a stuntman who vanished from a film set shortly after completing a dangerous stunt, they discover that he received a death threat minutes before his disappearance.

As the team investigates the disappearance of a divorce court judge, their suspects include a long list of husbands the judge ruled against in recent cases as well as an unknown man who was recently seen threatening him.

The team searches for a teenage girl who disappeared during her prom after reportedly leaving the festivities to rest alone in her hotel room upstairs.

The team searches for a missing 13-year-old girl whose mother fears fell prey to a fierce neighborhood drug dealer, and Jack tries to figure out how to protect Elena from her vindictive ex after her legal case against him falls apart, on the fifth season finale.