The episode begins with Irene telling Holmes that this isn’t how she wanted to reveal herself to him, but Isaac forced the issue. Holmes wants to why she seduced him and then led him to believe that she was dead. She tells him that he is the detective, so he should be the one finding answers. Holmes figures that he must have interrupted one of her plans. She tells him that he interrupted her “several” plans, several assassinations that she had meticulously planned. She tells him that initially she had planned to kill him but when she got to know him, she became more curious about him.
She felt that his mind was too beautiful and complicated to be destroyed, so she devised a way to study him in his own environment. She tells Holmes that he wasn’t as much a threat as he was portrayed to be. That is why she let him go. She also says that he proved his inferiority by disappearing into the syringe (by taking drugs). When she heard about his recovery, she wanted to see it for herself and that is why she came to New York. She says that she will never kill him because he is a work of art that she appreciates, but she will hurt him in ways that he will never be able to imagine. She leaves. Later, Watson arrives home. Holmes tells her everything. She removes the bullet from his shoulder. She asks him about his next move.
Later, Holmes turns in Isaac’s body to the cops. Gregson, who now knows about everything, finds it all confusing. He asks Holmes where they need to start looking. Holmes doesn’t know. He goes through Isaac’s stuff. Holmes tells Gregson that Moriarty/Irene took Isaac’s phone and wallet. Holmes notices some other stuff kept on the table and it catches his attention. The coroner tells him that these stuff belong to the dead men who were brought in last night. It is gang related. Holmes refuses to believe that. Holmes tells Gregson that the dead men’s cell phones are modified, exactly the way Moran’s and Gottlieb’s were. He turns on the phone and finds a coded message. This proves that the dead men worked for Moriarty.
He tries to break the code. It says: BN23 MACEDONIANSUN. Holmes figures out the message. The Macedonian Sun is a container ship which operates on Bay 23 North. It is a part of the fleet of Hellenic exporters, a company owned by Christophe Theopulus aka Narwhal. Narwhal who was a smuggler once, dropped out of that business and he now heads the International Shipping conglomerate. Holmes thinks that Narwhal could be Moriarty’s partner and he could help her move weapons or personnel though his ships. He tells them that the Macedonian Sun is supposed to arrive at the port this evening. Bell, Holmes and Watson are at the port, awaiting the ship’s arrival. Watson steps out to get something to eat.
Later, they see Narwhal arrive at the docks. They close in and check the containers. Instead of weapons or personnel, they find some lemurs. In the interrogation room, Narwhal tells them that he hasn’t heard of the name Moriarty. He tells them that the lemurs were for his daughter and son-in-law who live in Westchester. They breed rare animals on their ranch. He also tells them that his daughter, Alethea, is on a vacation in Kenya. Holmes wants to go to Westchester to confirm this information. Watson insists on changing the bandage before they leave. Watson gets a call from her brother. He tells her that their mother fell down and is now admitted in the hospital.
He tells Watson to check on her because he is in Barcelona for a conference. Watson tells Holmes that she will meet him in Westchester in an hour. Watson is on her way to the hospital when Moriarty stops her. She tells her that she was the one who called her brother about their mother. She says that she wants to talk to her. They go to a crowded restaurant and Moriarty tells Watson to tell Holmes to stay away from interfering in her business. She knows about that they surveilled the container ship and also interrogated Narwhal. Watson is surprised that Moriarty knows this. Watson thinks that Moriarty is afraid of Holmes.
Moriarty tells her that she is afraid of what she will do if Holmes continues to meddle in her business. She leaves. Bell and Holmes go to Westchester to meet the son-in-law. Holmes goes through the cabinets and finds it strange that his wife hasn’t taken her most crucial meds along with her to Kenya. He figures out that something is not right. The son-in-law tells Holmes that last week two masked men broke into the house and kidnapped Alethea. He says that his father-in-law came home the next day and told him that he was contacted by the kidnappers and told him that he will take care of everything. He did not want the cops to be involved. Watson calls Holmes and tells him about her meeting with Moriarty.
At the precinct, Gregson tells the duo that they will be getting their own security details until this whole thing blows over. He also tells them that Narwhal made bail after they left but he is not at his apartment and no one knows where he is. So, it looks like Narwhal is not Moriarty’s accomplice, he is her victim. Holmes thinks that Moriarty has some grand plan. Bell tells Watson and Holmes that they hacked into Narwhal’s computer and they found that he has been communicating with Moriarty. He also shows them the picture of a guy that Moriarty sent him. He says that the rest of the emails were encrypted and could be hacked into.
Elsewhere, Moriarty meets Narwhal and tells him that she wants him to kill the man (whose picture she sent him) and his family. She tells him that she will return Alethea once the work is done. Narwhal agrees. The next morning, Holmes tells Watson that he has deduced Moriarty’s plan. The man in the picture is Andrej Bacera and his mother is speaker of the Parliament of Republic of Macedonia. Andrej works as a vascular surgeon in New York and serves as a non-official diplomat when needed. Holmes explains that Andrej’s mother worked out a way for Greece to allow Macedonia into the European Union. This means that the currency of Macedonia, Macedonian dinar would change to Euro.
Less than 48 hours ago, a Swiss bank, acting on behalf of an anonymous client, purchased an enormous position in the currency. So, this means that someone is trying to manipulate the events to prevent Macedonia from joining the EU. He says that if Andrej is killed, then bad blood will reignite and dinar will remain the currency of Macedonia. Moreover, its value will soar and Moriarty will make a huge profit from her investment. At home, Andrej tells his Chief of Security, Jordan, that a man named Gregson is on the line and he is told him that a man named Narwhal will kill him. Jordan talks to Gregson. Jordan then puts Andrej and his wife in a safe room and lets Narwhal in. He tells him to finish it quickly. Narwhal goes inside and makes a 911 call.
He tells the operator his full name and says that whatever he is about to do, is for the love of his country. Narwhal shoots Andrej and his wife. Jordan sends a text. Narwhal receives a call from his daughter; she is safe and is with her husband. Narwhal hangs up and tells Jordan to “do it” quickly. Jordan shoots Narwhal. Later, Jordan makes a false statement to the cops. Holmes barges in and tells Gregson that Jordan works for Moriarty and he is lying. Jordan punches Holmes. Watson takes Holms to another room and tells him that he needs to stop. Holmes tells her that he almost stole opiates from a crime scene today, but he stopped because she would be disappointed in him.
But now, he is disappointed in her. Watson tells him to let Moriarty win. This is the only way it doesn’t eat him alive. Later, Holmes returns home and Bell asks him why he ditched his security officer. Holmes tells him that he wants to take a shower. Gregson calls Bell and tells him that a drug dealer around the coroner was beaten up. According to the witnesses, the perp was British and he was wearing a sling. Bell goes to the bathroom and kicks open the door. He finds Holmes lying on the floor. He has overdosed. Bell calls for an ambulance. At the hospital, Moriarty sneaks in to meet Holmes. She tells him that she did not want this.
She states that she literally begged him to stay away. She knew that her death would keep him occupied and that she could carry on with her projects, but she didn’t predict his descent into addiction. He surprised her, which is almost impossible for anyone to do. She wants him to go with her. Holmes tells her that both of them made the same mistake, they fell in love. He tells Moriarty that Watson figured her out and that is why she encouraged him to let her win. Moriarty realizes that Holmes faked the overdose. He tells her that now there are two people that could surprise her.
Watson arrives with the cops. The next day, Holmes is looking at his bees. Watson arrives and tells him that the recording from the hospital is giving Moriarty’s lawyers a tough time. Holmes tells Watson that the rare bee that one of his clients gave him, has managed to reproduce. He tells her that he is given the privilege to name it. He has decided to name the new species Euglassia Watsonia. The season ends.