The episode opens up with a the eponymous killer M knocking out a man, dangling him from a tripod, and pulling out a knife. Then we cut to the investigation where there is nothing at the crime scene but a large pool of blood. Sherlock Holmes immediately recognizes this M.O. M was a Serial Killer who had killed dozens of people in London by stringing them up, slashing there throats do they bleed and die, and dumping there bodies in the ocean. One of his victims was Sherlock's Love Interest Irene Adler.
Sherlock receives a mocking notes from M, not realizing he was caught on his security cameras. M is approached by a street vendor, and blows him off. This vendor is revealed to be an informant of Sherlock's. Using the scent of a towel Sherlock finds out the Hotel that M is staying at. At the hotel a woman steps out of the shower, and M walks up from behind only to hand her a roll of bills. She leans on him offering "another go", but he is to interested in the football game.
A woman hears her dog barking, and goes to check on it. She notices it has a hot dog, and asks how the dog got it. The woman is ambushed by M, who strings her up from his tripod. He is about to killer her when Sherlock shows up. Sherlock beats him with a baton, and drags him off to one of his father's warehouses.
In the warehouse, Sherlock has M chained to a wall, planning to torture and murder him. When asked about Irene's death, M claims he is innocent and a copycat did it. Upon farther interrogation, M admits that he is an assassin and that he has an employer. Sherlock does not believe this, but M tells him his name is Sebastian Moran and he was in prison for a football fight at the time of the murder. Sherlock looks this up and confirms that this is true.
Moran convinces Sherlock to spare him, because he can help him hunt down Moriarty but Sherlock stabs him in gut. Later we see him in the police station with a bandage around his torso. Moran claims that he lured Sherlock to the warehouse, a struggle ensued, and Sherlock stabbed him. Watson however points out there was no way Holmes could have inflicted such a clean wound without damaging an organ. Holmes is suspended from the NYPD.
This episode contains examples of the following tropes:
- Bald of Evil: M has a clean shaven head.
- Calling Card: M leaves behind pools of bloods after killing someone.
- Double-Meaning Title: "M." neatly sums up all the different forces intruding on Holmes and Watson's lives: M. Holmes, Sherlock's father; the serial killer "M", whose real name is Sebastian Moran; and Moran's boss, Moriarty.
- The Dragon: M AKA Sebastian Moran is this to Moriarty.
- Fakin' MacGuffin: "M" is a mysterious serial killer, who Holmes has a history and obsession with but who has never been caught, known only by that initial. Any viewer who knows anything about Sherlock Holmes would naturally assume that the "M" stands for "Moriarty". It's actually for Moran, The Dragon of Moriarty. And then subverted because Moran's murders were contracted kills on Moriarty's orders and with the notes he leaves behind all coming straight from Moriarty via email, while Moriarty himself is apparently the one who killed Irene Adler, meaning that, in a sense, Moriarty really is M.
- Football Hooligans: M's alibi for the murder of Irene Adler is that he was doing time for a Bar Brawl over the relative merits of Arsenal (his team) and Manchester United.
- I Choose to Stay: Not that we didn't see this coming already, but Joan at the end of the episode. Her six weeks contract with Sherlock is over. She decides to stay on anyway, going directly against Sherlock's father's orders.
- Mythology Gag: Teddy and the alluded-to network of similar street kids that Sherlock uses for surveillance around New York are an obvious nod to the Baker Street Irregulars.
- Psycho for Hire: M is a ruthless murderer who was killed dozens of people and makes them look like the random acts of a Serial Killer.
- Roaring Rampage of Revenge: Sherlock goes on one against who he believes to be Irene Adler's killer.
- Toplessness from the Back: Sebastian Moran's hooker.
- Wham Episode: Sebastian Moran shows up as a psycho serial killer. Sherlock catches him, tortures him and nearly kills him for murdering Irene... only to discover that Moran is not psycho, works as a hitman and did not kill Irene Adler, revealing his boss name: Moriarty.
- Wham Line: Moran drops one of these, revealing who killed Irene Adler:"Your girl. That was him. That was Moriarty."