Matt and Emily negotiate with a U.S. Customs Agent at San Pedro who takes his co-workers hostage after apparently trying to smuggle in a crate full of illegal immigrants. Meanwhile, Emily contemplates accepting a one-year special assignment that would mean being separated from Matt and is disturbed by his response.

A father turns to CNU to prevent a hostage situation after finding his teenage son's notebook full of violent images, but Matt and Emily arrive at the school after the hostage situation begins. The situation turns when one of the four gunmen shoots a hostage and takes his three comrades hostage as well.

Matt and Emily negotiate with two armed bank robbers who take a subway full of hostages. During the negotiation Matt is pulled away to deal with an hostage taker who Matt has met and successfully negotiated with, who has taken a therapist and the therapist's husband hostage. Matt talks the man who believes that an Evil Psychic Agent has taken the form of the therapist husband.

A woman, who is recently fired from a credit union, is wrangled into negotiating with a man who has taken her former co-workers hostage.

A seventeen-year-old boy takes hostages in a hospital operating room, demanding Dr. Khoury be found so that he can operate on his terminally ill sister. Matt and Emily attempt to save the hostages and help the boy.

After a sniper kills several people at random, the CNU seeks the suspect's hideout and believe they've caught him. When the suspect turns out to be a copycat and a police captain is shot, Matt and Emily work with Frank and Duff to find the real sniper before anyone else gets hurt.

A young boy is kidnapped from his parents at a fair and used as a ploy to obtain the attention of Emily after the hostage-taker sends a videotape to the media, showing the boy with a sign Ëmily Lehman did this". It becomes evident that the hostage-taker is looking for revenge as he uses the media to embarrass and humiliate Emily. He gives Emily and Matt a 24-hour deadline to find the boy. When the hostage-taker reveals more personal details about Emily's past, Emily decides to visit her sister, Allison, who is incarcerated at a federal prison. Allison refuses to help Emily, who had refused to use her FBI position to help her get out of her prison sentence.

Matt and Emily's negotiation with a drug lord goes awry when he escapes. When they finally find him in an isolated location in Mexico, Matt and Emily are stranded with two DEA agents and the fugitive after his associates arrived to save him.

What seems to be a textbook child kidnapping becomes a tangled mess when it is revealed that the victim is the daughter of David Lau -an Asian crime lord who is currently under FBI investigation.

Following a failed bank robbery which resulted in a hostage situation, Emily is taken hostage by the two bank robbers. Matt uses his people skills to negotiate with the robbers.

After learning that an illegal adoption agreement made between himself and a woman was a fraud, a man takes the woman's baby and the babysitter hostage at her home. When he makes contact with a radio personality, Matt and Emily are forced to negotiate live on the air.

The key witness in a federal money-laundering case and his wife are kidnapped and held hostage during the trial. Knowing the witness'value to the prosecution, the hostage-taker demands a $2 million ransom from the federal government. Matt and Emily, under Cheryl's leadership, join forces with Cheryl's ex-boyfriend, Sam, who is the FBI agent working on the case, to resolve the crisis.

The CNU resolves a hostage situation when a corporate executive takes 16 hostages in the company's boardroom. A second crisis involves a domestic situation that results in Matt and Emily questioning a decision they had made during the standoff. The second crisis soon turns into another crisis when the wife of the second crisis'hostage taker holds her husbands mother hostage in exchange for her "lover"who she supposedly was having an affair with. Matt is assigned to one scene and Emily who is no longer on the same hostage negotionating team takes the other as they attempt to solve both conflicts.

After a recent airplane collision, an air traffic controller is held responsible. He loses his temper and takes control of the air traffic control station in an attempt to clear his name.

A hostage situation arises at Dunne Hill Juvenile Detention Center when its inmates take several of the guards hostage. However, the teenage inmates'intention is not to escape from prison but to obtain the attention of the Senator to request the prison to be remained open thereby avoiding transfer to a Supermax facility. After Matt risks his job to help the kids Matt and Emily decide its best if they see other people.

As Darah, daughter of polygamous cult leader Warren Keegan, attempts to escape from her father and reunite with her sister, she is abducted by Warren and his three wives. Warren Keegan is wanted by the FBI after he assaulted a federal officer. By tracking the satellite dish Warren installed on his recreational vehicle, Matt and Emily are able to locate the hostage and her hostage takers. They find out from Darah's sister, who was Warren's wife before she escaped, that Warren believes that he could be saved from the apocalypse if he had four wives. However, Warren's actual reasons behind his marriages are unknown to Matt and Emily, and Warren's wives.

Matt Flannery and Emily Lehman, two FBI agents specialized in crisis negotiation, are negotiating with a television soap opera actor who is about to lose custody of his sons. After it is resolved, they are sent to negotiate with the son of a state senator who takes hostages inside of a coffee shop using a home-made suicide bomber vest.

The victim of Matt and Emily's hostage negotiation case becomes the target of a stalker. Although Emily doubts the woman's claims due to her feelings for Matt, Matt is determined to protect the woman.