Lewis and Sheppard investigate the shooting death of a man in his own home. The long-standing rivalry between the victim and his identical twin brother leads them to a reason for the killing. Ballard and Gharty team up with a narcotics detective from Washington, D.C. to check out a teenager's fuzzy account of a D.C. drug buy that led to his friend being shot and killed. Mike surprises Gee with news of his transfer into the BPD as an FBI agent liaison, and Gharty decides to leave his wife.

A man is shot and killed when a team of bounty hunters raids a house looking for a bail jumper. Falsone and Stivers quickly arrest one of the team members, P.J. Johnson, as the shooter, but he soon jumps his own bail to look for the fugitive. The detectives and team leader Dennis Knoll form an uneasy partnership to find Johnson, but their chase turns disastrous with a car wreck that leaves Lewis and a woman seriously injured. Gharty's mention of his Army service during the Vietnam War leads to relentless pestering from Munch, who does not believe his accounts, and Gaffney starts leaning on Mike to give him inside information on the performance of Gee's shift.

Lewis and the injured woman are rushed to the hospital and Johnson is re-arrested. Mike insists on taking responsibility for the accident, even after the woman dies and her husband files a wrongful-death suit against the department. Once Knoll and Mike work with Falsone to discover that the original fugitive has fled to Miami, the two of them head south with Bayliss to bring him back. The resolution of the cases leaves a bad taste in everyone's mouth, though. As Gharty's wife files for divorce, he decides to spend all the money he can in order to keep her from getting any of it in the settlement.

The discovery of a hastily buried newborn behind a motel leads Falsone and Stivers to a teenage couple, Debbie Straub and Craig Halpern. Although both of them insist that the baby was stillborn, the autopsy points to homicide. The case brings Mike Kellerman - now a private investigator, hired by Debbie's parents to clear her name - to the squadroom in search of information. His arrival rankles most of the squad, and Gee orders Falsone and Stivers to tell him nothing. After Danvers gets indictments against Debbie and Craig, Kellerman advises the Straubs not to bail their daughter out; soon afterward, she calls home and offers to testify against Craig.

Debbie testifies against Craig as part of a plea bargain, resulting in his conviction on a murder charge, but Falsone is not satisfied with the outcome. A visit with Craig reveals Debbie's involvement in the baby's death; shortly afterwards, he hangs himself in his cell. Sheppard's curiosity about Kellerman's departure from the squad stirs up bad feelings all around, but she lends him a sympathetic ear at the Waterfront. Falsone's contempt for his former coworker softens after Kellerman brings in voice mail recordings that show just how thoroughly Debbie manipulated Craig.

Called to the scene of a hit-and-run fatality, Munch and Mike are hard put to decide if the death was accidental or deliberate. Gharty recognizes the victim's knife and tattoo as marks of military service in Vietnam, and Munch confirms this after a look at the man's service record. The death turns out to be an accident, caused by a teenager joyriding in a stolen car. Munch obtains Gharty's record as well, sparking curiosity about the "other than honorable" discharge he received. Gharty snaps and tells the whole story: he saw American troops massacring Vietnamese civilians and tried to stop them, only to be ordered off the scene. Sheppard is cleared to return to full duty, but becomes angry at Lewis' reluctance to partner with her.

Bayliss and Ballard take the case of a bride-to-be found dead at the bottom of a cliff. None of the evidence conclusively points to homicide, suicide, or an accidental fall, and even the capture of a mugger fails to resolve the case. Ballard admits to Falsone that it has touched a nerve for her because she ran out on her own wedding. Sheppard and Mike are called to a movie theater in which one of the customers is found dead in his seat. The man had a habit of yelling out endings to the films; fed up with this behavior, the manager laced his popcorn with a sedative overdose. Gee's daughter Charisse gives birth to a son.

Detectives from Baltimore and New York continue investigating the deaths of both a government official and her killer. They eventually discover that the plot to commit the original murder started with allegations of sexual discrimination within the office of the White House Chief of Staff. However, an independent counsel looking into improper behavior in the White House takes over the case, frustrating Danvers and McCoy in their efforts to prosecute the murders. Meanwhile, Danvers comes up for a judicial appointment, but loses it after details of his juvenile criminal record come to light. Gee begins to regret allowing Mike to work with the unit after Mike's reports to his FBI superiors help to derail the prosecution.

This is part two of a two-part episode that begins on Law & Order.

A woman comes to Falsone and asks him to reopen the case of her younger brother's 1972 death - an accident she caused, according to her mother. The case stirs up painful memories for Gee, who had been its primary, and he, Falsone, and Stivers eventually learn the truth: the mother battered the boy to death and blamed her daughter. Bayliss faces widespread ridicule and criticism within the department after word spreads about his personal website, which includes his musings on sexual and spiritual matters. Warned by Gee that it may jeopardize his career, and reeling from his sudden rejection by a gay sergeant trying to stay in the closet, he decides to shut the site down. Falsone and Ballard reconsider their secret relationship after Stivers spots them together at dinner.

A man takes his two children (son and stepdaughter) hostage, shoots and wounds a cop when the Quick Response Team arrives, and then demands to negotiate with Mike. Mike learns that the man has acted out of desperation over being laid off and his wife leaving him. When his wife breaks through the police line, he shoots wildly out the window and kills her, a fact that Mike works desperately to hide from him. The man offers to trade his gun for a pizza, but breaks the deal and lets his stepdaughter go before killing his son and himself too quickly for the QRT to react. Mike berates himself for missing a chance to save both children, even if it would have led to the man being killed by the QRT.