We open on the windshield of a blue Mercedes covered in parking tickets. A "Final Violation" sticker stuck to the driver's-side window, a tow truck begins to lifts the car up. Inside, a male body is strapped into the front seat -- the head encased in a plastic bag, wrapped with duct tape at the neck.
In his loft, Castle sits across from Clark Murray, a top forensic pathologist. Castle is showing Murray morgue photos of a stabbing victim -- Beckett's mother, Johanna. Even though the case has been cold ten years, Castle is hoping Murray will find some vital clue that had been previously missed. Murray reminds Castle that the odds of finding a killer after ten years are astronomical.
After Murray leaves, Martha admonishes Castle, telling him that he needs to let Beckett know what he's doing. Suddenly, Alexis comes running in to announce that Owen has asked her to the Junior-Senior prom. Castle gives his blessing, but only if Alexis promises to stay out past her bedtime and have a good time. Martha is appalled that Castle is letting Alexis go out with someone he's never met.
At the impound lot, CSU photographers take pictures of the blue Mercedes as Castle and Beckett approach. Despite Castle's request, Beckett refuses to run a background check on Alexis's date. Ryan and Esposito tease Castle that if they had a daughter Alexis's age, they'd never let her out of the house.
They identify the victim as Dr. Joshua Leeds, a plastic surgeon. The few hundred dollars in his wallet indicates it wasn't a robbery and the bag over the head indicates it was personal. Lanie estimates Leeds has been dead a week and, before he died, his fingernails were removed and each finger was broken. In other words, he was tortured.
Leeds' fiancée, Courtney Morantz, identifies the body. She's devastated -- they were getting married in a month. She says Josh was never in contact with any criminal elements. Right before he disappeared, he was heading out to meet Courtney for a cake tasting. He never showed up and didn't answer his cell phone. What's more, Courtney has no idea how his car could have wound up on 133rd Street, since he worked in Midtown and always took the Midtown tunnel to the L.I.E.
Ryan and Esposito return from their canvas with nothing to report. Locals only remember seeing the car after it got the tickets. Esposito reports that Courtney's story checks out. So how did Dr. Leeds end up on the street in Harlem?
On their way to Leeds's office, Castle asks Beckett whether she's ever given thought to re-opening her mother's case. Beckett warns Castle that if he touches her mother's case, then their partnership is over. It took her a year of therapy for Beckett to realize that if she didn't let the case go, it would destroy her.
Castle and Beckett visit Dr. Leeds's office and interview his three nurses: Mario Guerrera, Julia Hammond, and Maggie Dowd. The staff maintains that Leeds left the office like normal the day he disappeared. None of his patients ever had medical complications, although recently one patient, Jacey Goldberg, had begun threatening to ruin Leeds's life when he refused to give her a fourth facelift.
In the bullpen, Esposito and Ryan rundown the background on Goldberg. Her husband had her committed the previous month to Bellevue for psychiatric treatment for her plastic-surgery obsession and Dr. Leeds testified in support of her commitment. She was released three days before the doctor went missing.
Beckett and Castle question Jacey Goldberg. She's shocked at the allegation that she murdered Leeds. She threatened to ruin him, not kill him. Plus, she has an alibi: On the day Leeds was murdered, Goldberg was in the hospital, getting more plastic surgery.
At the precinct, Beckett and Montgomery work the murder board. If Leeds had a history of turning people down, Montgomery wonders whether there's someone else out there he pissed off. But considering the CSU on the car came black clean, Beckett thinks a professional must have done it. Could Goldberg have hired someone to do the job? By breaking his fingers, someone was definitely trying to send a message.
At a clothing boutique, Alexis steps out of a dressing room wearing a prom dress and feeling just a little awkward. When Castle tells her she looks great, she growls at him in frustration and heads back inside. Confused, Castle looks to his mother. Martha explains that body-image issues are an intrinsic part of being a woman. When Alexis emerges from the dressing room again -- this time looking youthful, sweet and demure -- they all agree that she looks prefect.
Ryan and Esposito scour Dr. Leeds's office and find nothing incriminating. The only thing he kept locked up was his checkbook. Ryan, however, discovers a medical file stashed among Leeds' wedding files -- a casefile with all the patient's personal information blacked out.
They ask Leeds's senior nurse, Julia, to examine the file. She doesn't recognize it, nor can she identify the procedure in question, but the patient was a male in his mid-fifties. She says that Leeds never operated without her. On the date of the procedure, March 18th, Leeds was supposed to be attending a panel on reconstructive surgery. Why would he lie?
In the bullpen, Castle and the cops talk about what they've learned about the mystery patient. According to the hospital, the operation lasted nine hours. However, neither the assisting nor the anesthesiologist was with the hospital or were Leeds' regular people. And the hospital patient information says they can't find any files at all on the operation. It looks like a dead end, until Castle suggests they try the one department where nothing ever falls through the cracks: Billing.
Beckett finds out that the patient's hospital bills were paid promptly via wire transfer. She has Esposito check the account number and he learns that the account belongs to the U.S. Attorney's Office. Therefore, the patient was likely in Witness Protection program and had significant threats made against them. All of which means, they have to find the witness before the killer does.
Because it's an ongoing Federal investigation, the Assistant U.S. Attorney in charge, Candance Robinson, refuses to reveal the name of the witness despite Beckett and Castle's best arguments. Afterwards, Castle offers an idea: Since Robinson's office deals almost exclusively with organized crime, another way to find the witness's identity could be to simply ask the mob. And it just so happens Castle knows a guy, a capo with one of the other crime families, who owes him a favor.
Castle meets his mob contact, Sal Tenor, at an old dive bar. Tenor is sure the witness is Jimmy "the Rat" Moran, a former underboss for the Spolano family. Rumor has it Moran turned state's evidence a few months back.
At the precinct, Beckett offers to use her government sources to locate Moran. When Castle asks if she's referring to her ex-boyfriend, FBI Agent Will Sorenson, Beckett wonders why that might be a problem. It's not a problem for him, Castle replies, but then again, he's not the one Sorenson wants to get back together with.
Beckett approaches Sorenson as he's leaving work and hands him a rainbow sprinkle doughnut. Sorenson wonders why she's "sugaring him up." Beckett explains she needs to talk to Jimmy Moran. Sorenson replies that he doesn't work organized crime cases, but Beckett knows he can pull some strings.
At Castle's loft, Owen arrives to pick up Alexis for their prom date. Castle busts out his video camera and starts filming, much to Alexis's chagrin. After they leave, Castle gets a call from Beckett. Sorenson got the U.S. Attorney's Office to agree to a meeting with Moran.
Castle and Beckett sit in her car, waiting in a parking garage. Castle notes the cliché nature of the meeting. And true to form, a black Suburban SUV with tinted windows pulls up. Sorenson ushers Beckett and Castle into the backseat, where they meet Jimmy "The Rat" Moran, his face obscured by a ski mask.
When Moran he finds out the way Dr. Leeds was killed, he starts to freak out. The bag and duct tape are his MO. They're sending him a message. And if they got to the doctor, they'll soon get to him. He demands the Feds get him out of here.
Beckett and Castle return to the precinct and share the bad news: They scared Moran so much, he now refuses to testify in the Federal case. Suddenly, Montgomery steps out of his office, looking grave. On the way back to the FBI safe house, someone pulled up next to the SUV and opened fire, hitting both Moran and Sorenson.
At the hospital, they learn that the shooter, wearing a mask, pulled up in a late-model sedan with dealer plates and opened fire with Teflon bullets. Sorenson is still in surgery, though Moran is going to survive.
Castle gives Beckett a pep talk, noting that what's so extraordinary about her is she never gives up and that's why she's going to find out who did this and make them pay. Just then, they get word: Looks like Sorenson is going to be okay.
It's late and the front door of Castle's loft opens to reveal Alexis and Owen arriving home from their prom date. They share a sweet, awkward kiss and then Owen leaves. When Alexis turns around, she sees her Dad nearby, happy to see her home. Castle realizes time is flying and soon Alexis will go to college, get married, have kids, and he'll only see her on holidays. Alexis promises she'll always be her dad's little girl.
Castle shows up at the precinct to find Beckett at the murder board. She's been there since four in the morning. Beckett figures the mole was someone they'd spoke to, possibly the Leeds' fiancée and Leeds' staff. But the fiancée has an alibi for the previous night and her phone records don't indicate any calls to unknown numbers. Beckett asks her guys to check the staff records again. She and Castle head off to interview Dr. Leeds' nurse, Mario Guerrera, since he has a suspicious sounding alibi.
Beckett and Castle arrive at Leeds's office and have begun interviewing Mario when they get a call from Esposito. He called the nursing schools again and this time, he asked them to fax pictures. The Maggie Dowd that works in Dr. Leeds' office doesn't match the picture faxed over from her nursing school -- they're two different people.
Castle then notices Dr. Leeds' business cards at the reception desk -- Dr. Leeds is affiliated with St. Marcus Hospital, the same hospital where Jimmy Moran is recuperating. If Maggie has a hospital ID, she could be there now, looking to finish the job.
At the hospital, we find Maggie Dowd dressed in hospital scrubs and holding a clipboard. She makes her way to a hospital room protected by two Federal Agents. They check her ID and let her through.
Maggie crosses to the bed where Jimmy "the Rat" Moran lies half-conscious. She pulls out a syringe and we see a flicker of panic in Jimmy's eyes. His EKG starts to speed up. As Maggie injects the sodium thiopental into Jimmy's IV tap, she relays a message from Junior: "Go to hell."
But as Maggie turns around, she discovers Beckett, Castle, U.S. Attorney Robinson, and the FBI Agents there. They arrest her for the murder of Dr. Leeds and the attempted murder of Jimmy Moran.
At the precinct, Beckett finishes interrogating "Maggie" and hands her off to Robinson. Beckett tells Montgomery that "Maggie" -- real name Carla Dante -- is turning state's evidence against the Spolanos. She'd been killing for the family for five years. She had been hoping to find pictures of Moran at Leeds's office and when she didn't, she went after Leeds. When he wouldn't talk, she killed him.
Meanwhile, at his loft, Castle is meeting with Murray again to discuss the Johanna Beckett case. Murray tells Castle that he noticed the first stab was a low-angle thrust to the kidney, which would have sent Johanna's body into shock. This was a targeted killing, not a random killing like the police concluded. In addition, Murray checked the City M.E. files and found three other similar stabbings around that time.
Afterwards, Castle stands looking out the window. Martha insists he tell Beckett about the new findings. The information could lead to her mother's killer. Castle tells Martha that Beckett swore they'd be through if he ever opened the file. But Martha insists that Beckett needs to know.
At the hospital, Beckett sits bedside next to Sorenson. They're joking and sharing a rainbow sprinkle doughnut. Just then, Castle shows up, asks to speak with Beckett. Out in the corridor, she notices Castle's seriousness and asks if something's wrong. "It's about your mother," he responds. And off Beckett's look, we end the season.