Standoff centers on Matt Flannery and Emily Lehman, top-ranked FBI crisis negotiators who are forced to come clean about their secret relationship after it is revealed during a tense hostage standoff that they are sleeping together. Too valuable as a team to be split up, they are now under the watchful eye of their boss and their colleagues. Standoff combines the crackling romantic relationship at its core with intense drama and humor as these negotiators vow not to cross the line and let their personal feelings get in the way of the job. But they learn quickly that, in life and in love, everything is a negotiation.

When Air Traffic Control error is blamed for a plane crash hugging 180 people, the controller at fault hijacks the control tower in defense of his innocence. The stakes are high as dozens of planes circle above, but when Matt and Emily learn that the hijacker's wife is having an affair, the negotiators realize that the pressures at work aren't the only issues the hijacker is coping with. The situation hits a little too close to home as Matt and Emily get a glimpse of what could happen when personal lives get in the way of careers, and Emily pushes a hesitant Matt to go public with their relationship.

What seems to be a textbook child kidnapping becomes a tangled mess when it is revealed that the victim is the daughter of David Lao - an Asian crime lord who is currently under FBI investigation. To save the young girl's life, Matt and Emily must compromise the investigation, infuriating the Crime Division's Chief, and deal with a corrupt father who doesn't want their help. With two FBI teams on opposite sides of the same case and a kidnapper who is more experienced than he's revealing, Matt and Emily have their hands full at work while keeping some secrets from each other in the bedroom.

When a serial bank robber hits a string of banks along the California coast, Matt and Emily are determined to catch the thief. But when a confrontation at the next target bank goes awry and Emily becomes a hostage, Matt has trouble putting his personal feelings aside. The chase is on and after realizing that the suspects are a couple in love, Matt uses his knowledge of mixing business with pleasure to catch the robbers before Frank and the team take them out.

When a girl's health takes a turn for the worse, a young boy takes hostages in a hospital to force a surgeon to operate on his terminally ill sister. But the renowned doctor is on vacation, and the remaining surgeons refuse to perform such a complicated procedure without his help. With lives on the line, Matt and Emily must appeal to the doctor's past and the young boy's future in order to save the hostages and prevent the boy from doing something he will regret.

When a mysterious sniperhugs a string of random people, CNU is determined to find the snipers hideout. But when they catch a suspect and announce their success, a police captain is shot and they learn that the man in custody is actually copycat. With the real sniper on the loose, negotiations arent enough and Matt and Emily must work with Frank and Duff to catch the hugger before he hurts one of them.

After a surrogate mother scams a desperate husband out ,000 for her newborn baby, the distraught man takes matters into his own hands. He shoots the social worker who arranged the illegal adoption and then flees, taking the newborn child and the babysitter hostage. The resulting high-speed chase ends at the scam artists home, where, in an attempt to defend his actions, the man calls shock-jock radio personality Avery Steeles show and his plight goes live on the air throughout Los Angeles. Matt and Emily must enlist Steeles help to negotiate the crisis over the airwaves, but this power to the people jock is anything but cooperative.

After Matt and Emily save a young woman from a hostage situation, they learn the woman could be the victim of a stalker. Although Emily learns the woman has feelings for Matt and could be making false claims, Matt is determined to save her again.

In a revenge-of-the-nerds case, Matt and Emily must negotiate with three armed teen geeks who have taken two athletes and a pretty girl hostage and are taunting them - live on a Web site they have set up via real-time video. And when CNU blocks the site, they threaten tohug the cool kids. For Emily, the case is personal: She had been bullied herself as a teen. Matt, on the other hand, had been a bully.

Just moments after she was fired, a worker at a credit union's headquarters takes a call at her desk - from an armed man in a branch office who wants to speak to her boss. But he has just left the office, and a hostage situation ensues. Meanwhile, Emily and Matt are at odds because she left his apartment early in the morning without waking him.

The tables are turned on Matt and Emily when a Mexican drug lord escapes during negotiations with Emily. The pair and two DEA agents soon catch the fugitive in an abandoned tavern in Mexico - then are surrounded by his cohorts while out of communication range with headquarters.

When a U.S. Customs and Border Protection agent tries to bring a foreign container into the Los Angeles port without an inspection, the FBI and police step in when the agent takes three of his own colleagues hostage. Meanwhile, Emily contemplates accepting a one-year assignment on a Special Task Force in Quantico that would mean being separated from Matt and is disturbed by his response.

Two bank robbers have taken twenty-five hostages on a train, but Emily must handle the negotiations by herself, as Matt has been called away to another hostage crisis. However, when she suspects that the entire stunt is merely a decoy so that the real thieves can get away, things become much more complicated. Meanwhile, Matt must try to convince a psychiatric patient to release two people that he has taken captive.

When a fanatic polygamous cult leader abducts one of his daughters, who had tried to escape, Matt and Emily track them and discover a plot for revenge that could lead to the passings of many other people.

When a young boy is abducted from the Santa Monica Pier, Emily is thrown into the middle of the crisis. The situation becomes volatile when her personal life is brought into the public eye and she must confront her demons in order to save the child.

Cheryl becomes personally involved in the case after the key witness in a federal money-laundering case and his wife are kidnapped and held hostage.

A hostage crisis at a juvenile-detention center is sparked by a sensitive, intelligent teen who demands that the facility remain open. But his plans to keep the inmates from being transferred to a more crowded facility are thwarted by a thuggish teen. Meanwhile, Matt and Emily must fill out partner-evaluation forms. One question asks whether there's any situation the two can't resolve, and Matt answers no, but he does so before this situation unfolds.

Series finale: Having broken up as a couple, Matt and Emily decide they want to break up as a team as well. So Cheryl sends Matt out without Emily to defuse a crisis involving a distraught filmmaker, who makes racy videos, and his equally distraught wife, who runs the business. But one hostage situation soon becomes two, and Cheryl must call in reinforcements.