Beckett accepts Castle's marriage proposal, before moving to Washington DC for her new job, where she begins training and meets her new partner, Rachel McCord (Lisa Edelstein). After six weeks apart, Castle surprises her at her apartment, where he causes some trouble when he attempts to help her with a classified case. Castle returns home to discover that Alexis has brought a new boyfriend, Pi, back from her trip to stay with her. Castle is soon taken into Federal custody, where Beckett tells him he was exposed to a deadly chemical agent and has only one day to live.

With Castle having less than 24 hours before he succumbs to the effects of a deadly toxin, Beckett and McCord race against time to track down both the toxin and the antidote to save him and prevent more people from being killed. Their search takes them deep into a mystery involving a highly classified military base, a secret mission, and a coverup that reaches the very top of the Department of Defense.

With Beckett still in D.C., Castle insinuates himself into Ryan and Esposito's latest investigation, the murder of former child star Charlie Reynolds. The case is soon taken over by Beckett and McCord when evidence ties Charlie to the Russian mafia, and Beckett is confronted with an ethical dilemma that ultimately costs her her job with the Attorney General.

Castle is called in to negotiate a hostage crisis involving a murder suspect who will only speak to him, and puts his life in danger when he exchanges himself for two of the hostages. Castle believes she is innocent and discovers she was framed for murder. Gates allows Beckett, fired from her federal job after what happened in the last episode, to assist with the investigation, even though budget cuts have prevented her reinstatement to the precinct. With the case resolved upon the real culprit being apprehended, Beckett is returned to active duty thanks to the support of an influential man met during the investigation who turned out to be the long-lost biological father of the murder suspect.

The initial suspect in a grisly murder, Simon Doyle (Joshua Gomez), claims to be a time traveler from the future who has come back to prevent a disaster. Castle is intrigued while Beckett is dismissive, but their investigation eventually leads them to the true killer, and events begin to play out eerily similar to Simon's stories.

Castle and Beckett are called to investigate a murder where the victim was left in a crucified position, and discover her death was related to the search of a Freemason treasure. Meanwhile, Castle's relationship with Alexis breaks down when he insults Pi.

Alexis and a professor are investigating the case of a man on death row in Pennsylvania, and when his exoneration is denied, with only three days until the sentence is carried out, she enlists Castle's help, even though she is still angry at him. When they begin to dig into the case, they encounter resistance from the townspeople, but with help from Beckett and the team, they uncover details that the local police overlooked, and find that the situation is much more complicated than it looked.

Castle and Beckett investigate the murder of a popular couples' and relationship therapist. At first they believe the killer might have wanted her high-profile client list. Though, after further investigation it seems that he was after a rare, and pricey object that was in her possession.

A murder victim bears an exact resemblance to Lanie. Investigation soon leads to another victim who resembles Esposito. The only connection between the two victims is plastic surgeon Dr. Kelly Nieman (Annie Wersching), who apparently has no motive. Castle believes this has something to do with Jerry Tyson (known as the Triple X Killer) whom everyone but Castle believes to be dead. The team discovers too late that the Lanie and Esposito doubles were used to destroy all evidence of Tyson's crimes before they were murdered by his acolytes. Nieman escapes before she can be apprehended, leaving behind a flash drive intended for Castle and Beckett. Its seemingly innocuous contents leave Beckett deeply disturbed.

A man stumbles into a church carrying a baby boy before dying from gunshot wounds. When Beckett's team investigates, they discover that the victim was involved in a hostage situation and rigging the lottery.

The team searches for a murderous arsonist when it is learned that the victim of a building fire was shot to death. Meanwhile, Ryan's wife Jenny (Juliana Dever) goes into labor, as he and Esposito become trapped in the latest fire.

Jackson Hunt (James Brolin) returns to New York City with a mission to locate an Iranian intelligence officer. Disavowed by the CIA, he becomes the prime suspect in the murder of a computer hacker, with the investigation being led by Beckett.

The 12th Precinct takes the case of Mandy Sutton (Alexandra Chando), a teenage pop star whose rise to fame brought with it media attention. This case started after her body double Claire Samuels was found dead in an alley. Meanwhile, Beckett experiences the perils of being engaged to Castle first-hand when tabloid reports emerge of Castle reuniting with his ex wife.

Castle and Beckett investigate a murder in the competitive world of high-end fashion, after magazine editor Matilda King's (Frances Fisher) assistant is found dead.

Castle and Beckett are called in when two teenage girls witness a friend being killed by telekinesis during a video call.

What starts out as a straightforward murder case takes a turn towards the perplexing when three people all confess to the crime – and while all three know details of the murder that only the killer could know, each exonerates the others. Meanwhile, Alexis struggles with her guilt and her newfound independence after her relationship with Pi breaks down.

Beckett is recruited for a dangerous undercover operation with the aim of stopping a near-mythical drug baron. With no support, no intelligence and no assistance from Castle, she must unravel a conspiracy that leads back to Senator William Bracken and his bid to become president.

A Japanese woman named Jade is killed while looking for those responsible for her parents' deaths when she was young. Castle finds the murder weapon, but it is taken out of his hand by a ninja. The investigation leads them to a Mr. Saito, who is affiliated with the yakuza. He is killed and Castle and Beckett would also have been killed, but they are saved by Jade's sister, Saya, the ninja. The killer was an American contractor for the yakuza.

A 9-1-1 call leads the team to a Wall Street broker's body. The caller works for the U.S. Attorney's office, alongside Gates' sister Elizabeth (Salli Richardson). The victim was their insider, investigating his boss. He made a $25 million wire transfer, given to him by his boss, and planned to take the money home to Venezuela. However, Elizabeth's partner believed the brokerage still needed investigating and killed him for "the greater good".

Beckett is temporarily put in charge of the precinct while Gates leaves for a conference, and she and Castle are called in when construction workers unearth the remains of 1970s crime boss Vince Bianchi. His consigliere, Harold Leon (Jon Polito), is delusional and thinks it is still 1978. The detectives, with Martha's assistance, must re-create the era in costume and attitude so that Harold will fully cooperate in the cold case with Ryan and Esposito taking on Starsky and Hutch personas. The plan is a disaster when Harold clams up when Esposito breaks character and Gates returns early while the recreation is still going. Harold then tries to kill Vince's successor at a disco and it is discovered he was faking his delusions. Harold admits he forced himself to continue living like it was 1978 because he hoped it would help him discover the truth himself, and reveals he and Vince shared a secret that factored into his boss's death, which provides the clue that allows Castle and Beckett to solve it.

A competitive skateboarder's murder is investigated, which points to the unexplained death of a young boy in the past.

Following the events of "In the Belly of the Beast", Beckett carries out an off-the-books investigation attempting to connect drug baron Vulcan Simmons to presidential candidate William Bracken. She becomes a fugitive when the man she believes can lead her to Bracken is murdered. This forces the elusive Mr. Smith to come out of hiding and reveal a key piece of evidence that could get Bracken brought to justice, if Beckett can find it first before her pursuers find her. When Beckett is caught, she finally finds evidence to arrest Bracken. The evidence is a tape recording Roy Montgomery had left for Beckett's mother, where he confesses to various crimes including planning Johanna Beckett's murder. With the new evidence, Beckett is cleared and she is finally able to close her mother's murder case, arresting Bracken on live TV as he announces his plans to run for president.

With Bracken in custody and a light caseload, Castle and Beckett turn their attention toward finally getting married. However, complications ensue when they discover Beckett has been legally married to another man the last fifteen years. After finally working everything out, tragedy seems to strike when Castle's car is run off the road by an unknown assailant, leaving him apparently trapped in a fiery wreck.