|"Enough Nemesis To Go Around": While protecting Karen Lloyd, former bookkeeper to drug lord Elana March who is set to testify against her, Bell and Watson discover that Lloyd and her police escort are mysteriously shot in an elevator. Two months later at the 11th Precinct, Bell and Watson are still puzzled by the elevator shooting. The elevator didn't stop, no one entered and the bullets wounds reveal the shots were horizontal. At the precinct, Gregson tells Bell and Watson a tip on the elevator shooting named a hotel guest, Kevin Elspeth. The name of the tipster is familiar to Watson. Bell and Watson question Elspeth and show video of him checking into the hotel the day Lloyd was murdered. When asked why he used an alias, he indicates that he hires hookers. They point out that he uses aliases in many hotels and all locations had a murder committed when he visited. He knows about Lloyd's murder but admits no wrong doing. Outside, Bell notes how suspicious Elspeth is and parts ways with Watson. Discovering a large magnet was used in the murder, Holmes discovers evidence of Elspeth's guilt. He confesses and implicates March who Bell and Watson arrest.
"The Five Orange Pipz": At the precinct, Bell watches as Captain Gregson interviews Kitty Winter and kids with Holmes that he's really back working with the NYPD again. Later, Gregson and Bell are at the office of lawyer Theo Fordham, attorney to Elias Openshaw, where he's been shot and a package with five orange beads is spilled in front of him. Kitty examines Theo's murder scene and reacts strongly when Bell touches her arm. Bell and Watson discuss their negative initial impressions of Kitty. Bell brings in a taxi driver, who he saw from traffic video, hit a pedestrian. The driver, Azeem, admits that Openshaw ran in front of his vehicle and he hit him. He tried to help him, but Openshaw saw a woman, who Azeem identifies as US Attorney Angela White, and fled. Confronting White, she denies seeing Openshaw when he was on the lam even though the offices of her campaign for Congress are close to the accident scene and, she orders them to leave.
"Just a Regular Irregular": After finding a dead body while on a math puzzle hunt, at the precinct, Harlan Emple explains to Bell and Gregson that math problems were posted at locations which, when solved, would reveal the location of the next problem. Frustrated that Bell and Gregson believe he murdered the person he found, he demands to speak to Holmes and Watson. Arriving at the station, Holmes explains that Emple is one of his "Irregulars." He isn't happy to see Emple and unsuccessfully tries to get out of accompanying Bell and Emple to the crime scene. Learning of a suspect, Byron Lowenthal, Bell knocks on Lowenthal's door. Holmes pulls Bell away and moments later, a shotgun blast blows a hole in the door and Lowenthal flees. Emple solves a math clue Lowenthal was given which leads Bell and Holmes to a location where Lowenthal's body is found.
"Bella": After Edwin Borstein, the head of an artificial intelligence (AI) company with a unique program named "Bella" is found dead in the office containing Bella, Bell indicates that Borstein died of an epileptic seizure. Holmes finds that a music CD sent to Borstein by Michael Webb had a virus on it which caused an epileptic fit which killed Borstein, Webb is questioned at the precinct by Bell and Gregson. He admits to sending it but not to creating a virus that would kill him. Erin Rabin, a philosophy graduate student, and devotee of computer science professor Isaac Pyke, was found to have been in Webb's apartment. Bell questions her and Pyke as they exit one of his classes. She confesses to Borstein's murder and insists Pyke had nothing to do with it. At the precinct, Bell question Rabin who freely admits her guilt, even though she can't demonstrate any programming skills.
"Rip Off": Called to the scene of a severed hand, Holmes quickly deduces that the owner is dead and leads Kitty and Detective Bell to a car impound lot where Holmes finds a handless body caught underneath a car, identified as Moshe Shapiro. At The Brownstone, with the use of a realistic dummy, Holmes shows Bell that ripping the hand off someone with a broken wrist is possible. He identifies a weightlifting gym near the site of Moshe's death as a possible venue for suspects. At the gym, Holmes tricks a weightlifter, Dana Kazmir, into giving a DNA sample which is a match for DNA on Shapiro's body. At the precinct with his lawyer, Kazmir confesses and they propose a leniency deal to Bell and Gregson in exchange for information. Later, Bell shows Holmes untraceable emails sent to Kazmir from "Mencius BlackBag", the man who hired him to kill Moshe. Blackbag is identified as Leonard Oosthuizen who is brought to the precinct and in "the box", is accused by Bell of Moshe's murder and conspiring to kill three others. Holmes believes Oosthuizen is innocent but Bell disagrees and intends to make Leonard confess. Later, Kitty and Holmes find evidence that an employee at Shapiro's store, Amit Hattengatti, is responsible for hiring Kazmir. He's arrested by Bell after being brought into the precinct.
"Terra Pericolosa": Bell arrives at the 39th Street Library after Kitty finds the body of security guard Gerald Vogel and comments that Holmes must be so proud of Kitty finding her first dead body. He questions Austin Cornblatt, who sold a rare book of maps and was catfished by Holmes into thinking he was communicating with a young woman.
"The Adventure of the Nutmeg Concoction": Discovering that a former crime scene cleaner is working for criminals and is cleaning the scenes with a special fluid, Holmes locates the cleaner, Conrad Woodbine, whose is questioned at the precinct by Bell and Gregson but they're unable to elicit a confession from him. Later at Woodbine's home, Holmes finds an artificial tendon in a drain which Bell later identifies as belonging to Woodbine who was killed and his body dissolved using his concoction.
"End of Watch": After Officer Alec Flynn is killed and found to have been armed with an air pistol, Bell and Watson question his wife, Brie. She admits that after a football accident, Alec became addicted to Oxy. However, he recently became sober, came back home and was proud to return to active duty and leave the NYPD armory. Holmes is called to the precinct by Bell, where he introduces ATF Agent Hernan who identified Alec's killer as Niko Buros. Buros trades guns for drugs with a Mexican gang and an ATF raid captured nearly a thousand of his weapons. At the armory, Bell and Watson question Officer Doud, Hatem's uncle who angrily denies any connection with Alec or Buros. Alec's drug dealer, Charlie Riggs, is questioned in "the box" by Bell, Holmes and Watson where Holmes realizes Buros' target is the armory, which he robs. Kitty, Holmes and Watson are able to deduce how Buros intends to smuggle the weapons out of the country and Bell and a police team arrest Buros and parade him in front of dozens of officers.
"The Eternity Injection": After a friend of Watson's, nurse Marissa Ledbetter, is found dead, a list of dosages if found on her body and DNA from a Chris Jacoby under her fingernails. Bell questions Chris' wife, Sarah, who reported Chris had gone missing days before. Discovering that Chris and others were participating in an illegal drug trial, Holmes and Watson find a survivor of the trial, Louis Carisle. Bell and Gregson question him and learn details of the trial and get a description of the doctor who was running it. Bell arrests the doctor, Dwyer Kirke and learns that the drug allowed "time dilation" to be experienced. Kirke provides details of the trial but refuses to reveal who is behind it. Holmes and Watson find a suspect, James Connaughton and Bell questions his nurse, Brett Won, who reveals that Connaughton is behind the trial. Bell, Holmes and Watson arrive at Connaughton's to arrest him but discover he has taken the drug and will likely remain in a coma for the remainder of his life.
"Seed Money": At the scene of the death of an elderly couple, Watson speculates they committed suicide but Holmes leads her and Bell into the building's basement where a burned body is found. Checking the third floor, the body is found to be Clay Dubrovensky, who had a doctorate in botany and genetic engineering. An ex of Clay's, Courtney Stever, is questioned by Bell at the precinct where she indicates that Clay was growing marijuana for a drug gang, SDS, and he also engineered new strains of pot. Barbara Conway, a senior VP at AgriNext is questioned by Bell, Holmes and Watson at her company's office. After two AgriNext executives are burned alive, Bell tracks down stores that sell a special rope used to bind the executives. This leads them to an SDS member who admits to many murders but not Clay's.
"The Illustrious Client": While Ron Davis is being questioned in "the box" as a suspect in the serial torture and killing of women, Bell asks Kitty if he was the man who abducted her. After Bell discovers prints on a phone from the location that Melanie Vilkas was abducted came from a violent ex-con, Simon de Merville, police raid his house. After Simon isn't found, Bell questions his sister, Violet, at the hospital she works at. From a phone call, Holmes deduces Simon is hiding in a land-parked boat which a Mr. Osweiler, Simon's past neighbor, confirms. Gregson calls Bell that the boat Simon was in burned, killing him.
"The One That Got Away": After Kitty recognizes Del Gruner as her kidnapper and a serial killer of women, Bell and Gregson question him in "the box." Del Gruner denies any involvement in several cases and his lawyer threatens to sue the NYPD. Tabitha Laird, a woman who works at a charity Del Gruner supports and who had a incident with him, is questioned by Bell, Holmes and Watson. At her home, she denies any issues with Del Gruner who invited her and her adopted son to his beach house. Later, believing that Laird's son is Del Gruner's from a woman he abducted and raped, Bell, Holmes and Watson convince her to provide a sample of her son's DNA.
"Hemlock": Bell helps Holmes run down leads in the disappearance of Steven Horowitz. Finding that Horowitz was keeping up the fiction he worked for a law firm while running a debt collection company, Bell finds and questions one of his employees, Eduardo Peña. Eduardo unwillingly provides the latest debt package they were trying to collect from. Holmes and Watson show Bell that Horowitz had started to forgive people's debts and that the purchase of the latest package was financed by various criminal bosses.
"The Female of the Species": Bell meets Holmes at the zoo and agrees to work with him finding two stolen zebras. Examining the scene, Bell is miffed why Holmes won't call him by his first name. Tire tracks are found and Bell notices a distinct purple paint scraping on a metal gate which Holmes recognizes is used by the trucks of a delivery company, APD. At the Brownstone, Holmes has discovered from APD that one of their trucks was stolen eight days before and he's obtained the truck's manifest. From a pet collar with a GPS chip that the truck was carrying, he and Bell find the truck's load which has been dumped under an overpass. Shifting through the load, Bell gives Holmes advice on how to handle the stress Watson is experiencing. Holmes finds a receipt from a horse veterinary service and they proceed to its address. The vet service is located near a warehouse where Bell discovers the APD truck abandoned, with hay in the storage area. They find the two zebras, who have both given birth, but their offspring aren't there. Digging through a hay pile, Holmes finds a veterinarian, Dr. Chang, dead from a gunshot. Later with police on the scene, Bell reports that Chang had skin under his fingernails, likely from his killer. With a police team, Bell and Holmes search an abandoned hospital and one of the foals is found. However, Holmes points out that the foal isn't a zebra, but a quagga, which have been extinct since 1883. At the zoo with Bell, Holes deduces that one of the staff, Ben Reynolds, a PhD candidate is the kidnapper. Later, matching Ben's DNA to that under Chang's fingernails, Bell and Holmes find that Reynolds escaped from his home through an underground tunnel. That evening at the Brownstone, knowing that Reynolds must sell the quagga soon to finance his escape, Holmes gives Bell all case files on the sale of rare animals and proposes they look for an on-line code that would indicate such a sale. The next morning, Holmes wakes Bell using an alarm clock and Bell finds a note from Holmes telling him to meet at a café in Greenpoint. At the café, Bell sits with Holmes who has ordered him breakfast and explains it affords them the best vantage point for seeing Reynolds. Explaining that the phrase "once in a blue moon" was used on a web site to indicate an illegal animal sale, Holmes found Reynold's ad for the quagga, won the bid, arranged to meet Reynolds and called Gregson. While explaining, Bell sees Reynolds pull up in an SUV and meet a man who after seeing the quagga in the SUV back, waves his hat. Police descend on Reynolds and arrest him. Bell smiles at Holmes who shakes his hand and finally calls him "Marcus."
"When Your Number's Up": After a homeless man, Henry, is shot, at the crime scene, Gregson and Bell show Holmes and Watson the envelope found on Henry. It contains a note that rich people are worth more than the poor, a math equation and nearly $4000 cash. The formula is traced to attorney Arlen Schrader. At Schrader's office, Holmes expresses disdain for Schrader's profession while Bell realizes the killer "bought" Henry's life using Schrader's formula. Bell questions an ex-girlfriend of Schrader's, Erin Chatworth, who indicates he dumped her over a client, the crash of Aceway Flight 1059. Bell is at the murder scene of Freddy Duncan who had a relative die on Flight 1059. He's at the meeting with Aceway's CEO and attorney in which they explain different victim compensation methods they are considering. After staging an attempt on her life, Bell is one of those who examine the home of Dana Powell, whose husband died on Flight 1059. After finding evidence that Powell is the killer, Bell, Holmes and Watson show it to her and her lawyer and convince her to confess and make a deal.
"For All You Know": After Holmes is accused of murdering Maria Gutierrez several years before, Bell provides a list of those who frequented a soup kitchen Maria volunteered at to Holmes who recognizes his ex-drug dealer Oscar Rankin on the list. Bell is part of the team who arrests Councilman Robert Barclay for Maria's murder.
"T-Bone and the Iceman": After Allie Newmeyer is murdered after a car accident, Bell shows Holmes and Watson Newmeyer's body, which is frozen white. He also reports her car was hit by a white van. After finding the van was stolen from cryoNYC, a company that freezes bodies, and the body of Jim Sullivan was stolen, Bell reports that a cousin of his, Vance Ford, was found strangled. Bell and Holmes are summoned to cryoNYC with the report of a break-in. Employee Trent Resnick describes a man with a floppy hat as the intruder who attacked him and that he hit employee Ryan Lee in the head with a wrench. Later, Bell and Watson show Resnick that he's lying and he confesses to a plot with Lee that involved the murders.
"The View From Olympus": After Galen Barrow, a ride-share driver for the company Zooss, is hit by another car and murdered, Bell calls Holmes and Watson to the scene. Watson and Bell check out a lead on a yellow cab with front end damage but discover it doesn't fit the crime scene damage. Later, called to the precinct by Bell, they question Gordon Meadows, a registered sex offender who was blackmailed into killing Barrow. Bell, Holmes and Watson question CEO Eric Frazier and technician Brandon Felchek at Zooss' HQ and obtain all their company's data. Called to the precinct, Bell introduces them to Mahra Kemp whose brother Patrick worked for Zooss until he was killed in a mugging a month before. Mahra was questioned by Barrow after Patrick's death and she believes Barrow's death might be connected. At Zooss, Brandon Falchek meets with Bell, Captain Gregson, Holmes and Watson who tell him that they've found that he cut off Patrick Kemp's access to Olympus months before as he discovered he was blackmailing users. However, they've also found that Falchek stalked and attacked a woman named Felice Armistead who uses Zooss. Falchek is arrested and told he'll be part of a police line-up in which they believe Felice will easily pick him out as her attacker.
"One Watson, One Holmes": Bell calls Holmes to the murder scene of Everyone member "Species," aka Errol White, and Holmes finds hair matching that of Everyone member "Sucking Chest Wound," aka Petros Franken." Bell learns that blood matching White's was found in Franken's car trunk. Holmes believes Franken is innocent and is provided with a lead of an information stash of White's that Holmes believes was obtained by Caleb Hill. In hospital, having bought and crashed an expensive motorcycle, Bell, Holmes and Watson question Hill who obtained the stash weeks before White's death and turns it over.
"A Stitch in Time": Investigating the murder of Garrison Boyd, a debunker of myths, Bell and Holmes speak to a cult head, Finn. Holmes and Watson find that Boyd was killed over digging up a trans-Atlantic cable called "Ruby" and explain its importance to Bell and Gregson. Finding that Nadim Al-Haj dug up the cable and was going to attach a device to it, Bell finds that he's from Iraq and was an electrical engineer. Giving his file to Gregson and Holmes, it's found that Nadim lived in an apartment owned by another suspect, Colin Eisley. At Eisley's home, Bell and Holmes accuse him of employing Nadim to steal financial data with the device. Eisley doesn't confess but later, after Holmes deduces the device delays financial information, which would benefit Eisley, he's confronted again. Deducing that Eisley paid Nadim in art, which has been reported stolen so Nadim can't sell it, Bell, Holmes and Watson encourage Eisley to confess.
"Under My Skin": After paramedics are shot and their ambulance, with patient Maggie Halpern in the back, is stolen, Bell, Holmes and Watson review the security footage in which a man can be seen shooting the ambulance staff and driving the ambulance away. The shooter, Wallace Turk, is found but won't reveal where the ambulance is. Having found the ambulance from Holmes' lead, Bell shows Captain Gregson Halpern's body, which has been cut open. However, he's determined that Halpern was killed when Turk was in custody, so he must have a partner. At the Morgue, Dr. Hawes tells Bell, Holmes and Watson that Halpern's throat was slashed before she was cut open. Halpern's roommate, Paige, is disbelieving when Bell and Watson tell her that Halpern was a drug mule. Finding she went to Brazil for gastric bypass surgery, Bell looks into the surgeon. He and Watson visit the offices of dentist Marty Ward having discovered that Janko Stepovic, a drug gang leader, uses the offices for his business. They propose he help them retrieve the heroin so that his competitor's can't sell it. At the precinct, Bell is surprised by Ward, whose hand is heavily bandaged, and his lawyer, Sarah Penley. Penley asks for protection and immunity for her client in exchange for information. later, Ward is tricked into confessing and in "the box", Bell watches as Ward writes his statement. Once completed, Bell lets in an Asian detective who Ward sees posed as a Triad member and realizes his lawyer was right and that he's been duped.
"The Best Way Out Is Always Through": Exiting a concert, Bell and his girlfriend, Detective Shauna Scott make plans for the evening until they are both called to the crime scene. Arriving separately, Shauna and Bell don't reveal their relationship to Holmes and Watson as they examine the body, identified as Judge Dennis Vaughn. While Bell plans to get the list of those at the fundraiser to identify who the judge was with, finger prints are found on the screwdriver which Holmes can see are from a woman. Bell finds the prints on the screwdriver belong to a convict, Nikki Moreno, who escaped from Pemberton Women's Correctional Facility in NJ days before. At Pemberton, which is a for-profit prison operated by Reform Enterprises (RE), Deputy Warden Trey McCann indicates to Bell, Holmes and Watson that Moreno was a troublemaker. Bell and Watson check Moreno's cell. Watson tells Bell she knows he and Shauna are dating, which he admits to and is happy about. Bell and Watson question Jeff Harper who denies helping Moreno escape and doesn't know her whereabouts. They leave Harper's office and Watson tells Bell that Shauna works for Internal Affairs (IA). Bell meets Shauna at a bar and expresses his anger at discovering that she secretly works for IA and didn't tell him. Accusing her of being a rat, she counters with an incident in which Bell turned in a crooked commissioner. Feeling his trust in her has been betrayed and ruined their relationship, Bell walks out. At Pemberton, Holmes finds Moreno's body inside a recycling bin and shows Bell and Watson. Believing that a prison guard, McCann, worked for criminals incarcerated who wanted Vaughn dead, Bell and Holmes question a CAG executive, Perry Franklin, at his office. Franklin won't provide details why McCann was fired until threatened with media exposure. He then allows them to review hard copies of McCann's work files but insists none leave the premises. Discussing what happened with Shauna, Holmes comments that everyone he works with now has no love in their life, just like him. Despite her working for IA, Holmes encourages Bell to give his relationship with Shauna another chance. After finding evidence that Franklin murdered Vaughn, Bell, Gregson, Holmes and Watson show him the evidence and he's arrested by NJ police. Bell meets Shauna outside her precinct, apologizes and says he'd like to get back together with her. However, Shauna's reflected on Bell's accusations and tells him that she's quitting the precinct to work at IA full-time. She indicates she'll need some time before they can resume their relationship. That evening, a forlorn Bell arrives at the Brownstone and commiserates with Holmes. Throwing cards into the Stanley Cup, which Holmes has confirmed is real, Bell turns down an opportunity to meet one of Holmes' paramours and enjoys the distraction.
"Absconded": Investigating the death of USDA employee Everett Keck while he was inspecting bee hives, Bell and Holmes search for a bodyguard for a sheik, Rashid Musharakh, they are able to find him by tracking a laptop he traded for in a pawn shop. Later, Bell, Holmes and Watson show a professor, Tara Parker, the evidence against her and her husband and Bell arrests her.
"A Controlled Descent": After Alfredo Llamosa is kidnapped, Bell, Gregson and Watson question Neil Kopecky. Fired from Castle due to conflicts with Alfredo, Kopecky is defiant and uncooperative and won't speak without his attorney present. Holmes meets Oscar Rankin, who confesses to kidnapping Alfredo but demands Holmes' help for his release. Watson explains the situation to Bell and Gregson who are incredulous that Holmes is meeting with Oscar instead of turning him in. Watson asks that they help her find Alfredo while Holmes deals with Oscar. Bell and Watson examine Oscar's apartment but find little until Watson looks outside and sees the '73 Charger under a tarp. Inside the car, she finds a hamburger wrapper from Dilby's, which she tells Bell is only on Long Island. While visiting a construction site, Watson starts to lose hope that Alfredo will be found. As she stares at a coffin sized hole in the ground with Bell, she realizes that there are many cemeteries on Long Island. Several businesses that make headstones are also on the island that cut marble and granite. At South Shore Memorial, Bell, Watson and police find Alfredo tied up and barely alive.