In Minsk, Belarus, Sherlock talks to a prisoner, Bewick, and tells him to explain what happened, from the beginning. Bewick tells him that he picked up a woman at a bar, and she kept getting on him. He finally picked up a knife without realizing it, and stabbed her. As he talks, Sherlock can't resist correcting his poor grammar. Finally, Sherlock leaves, and Bewick insists that he'll be hung without his help. Sherlock pauses only long enough to tell him it's "hanged," not "hung," and departs.
John returns home to find Sherlock shooting a gun into the walls because he's bored. The Belarus case wasn't worth his time. John is even less thrilled when he finds a decapitated head in the fridge. Sherlock has read John's publication of their first case together, and complains that John thinks he is ignorant on certain things. He insists that it doesn't matter if the Earth goes around the Sun, what matters is his work, and without it, his brain rots. John storms out, going past Mrs. Hudson, who figures they had a domestic squabble. Sherlock looks out on the street and complains that it's too peaceful. As she leaves, an explosion goes off, blasting in the windows and knocking Sherlock down.
John goes to stay on Sarah's sofa, and she suggests that he might stay in her bedroom the next day. As they watch a newscast about the exhibition of a Vermeer, Sarah goes to take a shower and they run a broadcast about the explosion on Baker Street. John goes back to the flat and finds Sherlock stroking the violin and talking with Mycroft. Sherlock refuses to take on Mycroft's most recent case, insisting he has too much work, and dismisses the explosion as a gas leak. Mycroft tells them that a civil servant, Andrew West, was found on the Battersea tracks, his head bashed in. He was working on the Bruce Partington plans, part of a missile defense system. The memory stick with the information is missing. Mycroft wants Sherlock to take the case, but Sherlock refuses. As he leaves, Sherlock starts playing, badly. Once Mycroft is gone, John wonders why Sherlock lied and figures that its sibling rivalry. Sherlock's phone rings and he takes a call from Lestrade, and says he can't refuse. He invites John along with him.
At Scotland Yard, Lestrade tells them that the gas leak explosion was no accident, and the only thing that survived was a strongbox. Inside the box is an envelope addressed to Sherlock on paper from the Czech Republic. The envelope contains a pink phone like the one from "A Study in Pink." There is one voice mail, containing only five Greenwich pips. There's also a photo of an empty room. Sherlock explains that pips were used by secret societies to send messages, and realizes that it will happen again. He also recognizes the empty room.
Sherlock takes John and Lestrade back to Baker Street and has Mrs. Hudson show her the basement apartment. It's the room from the camera, and the door has been recently opened. Inside are a pair of trainers. As Sherlock examines them, the pink phone rings and a crying woman reads a message saying that the bomber has sent Sherlock a message as a little puzzle. Sherlock tells the others that he's been expecting the call from some time. The hostage reads the message, telling Sherlock he has 12 hours to solve the puzzle. She's fastened with explosives and trapped in a car.
At St. Bartholomew, Sherlock examines the trainers and dismisses the woman as irrelevant to the mystery. Sherlock's cell phone beeps and John confirms that it conations text messages from Mycroft. Sherlock insists that the plans have left the country and there's no point in his investigating. Molly comes in with her new boyfriend, Jim from IT, and Sherlock dismisses him as gay. Jim is impressed with everything he's heard about Sherlock from Molly. Once Jim leaves, Molly is angry at Sherlock for spoiling her relationship, and explains everything that lead to his deduction, including the fact that Jim left Sherlock his number. Molly storms out and John explains that Sherlock saving her time isn't kind. He then invites John to examine the trainers. John comes up with very little, and Sherlock explains that the owner treasured the shoes and had eczema. The mud on the soles shows it's Sussex pollen with London mud on top of it. Sherlock realizes that the shoes belonged to Carl Powers, a boy who drowned 20 years ago while swimming.
As they take a cab, Sherlock explains that Carl Powers drowned in 1989, and he read about Carl having a fit in the water and drowning. Sherlock realized that the shoes weren't there, but the police weren't interested in his theories. With five hours later, Sherlock returns to Baker Street and goes through his clippings, while Mycroft texts John since Sherlock won't answer his phone. When John objects, Sherlock sends John to deal with Mycroft and get more information on the case. John lies and says that Sherlock is handling the case. Mycroft isn't fooled, but explains that West was involved in the Bruce Partington project, and left his fiancée Lucy saying that he went to see someone. He tells John that West didn't have any ticket on him, and they need Sherlock to determine how West got to Battersea.
With three hours left, Sherlock finds traces of poison in the trainers and realizes that someone poisoned Carl with a deadly poison introduced into his eczema medication. He had a fit two hours later and drowned. Sherlock posts the solution on his web site, and the female hostage calls to tell them where she is, and that they can rescue her. The police bomb squad deactivates the bomb, and Lestrade calls in John and Sherlock. He explains that someone abducted the woman and planted her with explosives, and threatened to set them off if Sherlock failed to solve the case. Sherlock gets a new call with four pips, and a photo of an abandoned car. Donovan tells Sherlock that he has a call, and he takes it. It's a new hostage, who reads off a message that Sherlock shouldn’t rely on the police. Carl Powers laughed at the bomber, so he took revenge. Now he'll kill the new hostage if Sherlock doesn't solve the second case in eight hours.
Lestrade tracks the abandoned car to a yard. The man who rented it, Ian Monkford, has disappeared and his blood is all over the car, but there's no body. Sherlock has Lestrade send him blood samples and then talks to Mrs. Monkford. He claims that he knew Ian but knows nothing about him, and Mrs. Monkford talks about how her husband was depressed, and forgot to renew the tax on the car. Sherlock then leaves, explaining to John that people will tell you things if they can contradict you, and that she referred to her husband in the past tense.
Sherlock goes to the car rental agency, Janus Cars, and talks to the owner, Ewart. Ewart scratches at his arm and has a tan, and insists that he never knew Ian Monkford. Sherlock asks him for change for the cigarette machine, but Ewart shows him his wallet to demonstrate he doesn't have any. Sherlock then leaves with John, and explains that he now knows that Ewart is a liar. He returns to the lab and analyzes the blood from the car. Once he finds what he's looking for, he takes Lestrade and John to the car, and explains that there was exactly a pint of blood on the car. The test shows that it was frozen. Ian donated the blood several weeks earlier, and Ewart's people spread it on the car to make it appear that there was foul play. Janus Cars makes someone disappear if they have financial trouble. Sherlock explains that Ian is in Columbia, because Ewart had Columbian change in his pocket. He was scratching his arm because he had recently received a booster jab. Ms. Monkford will then split the insurance payout and meet with her husband.
Sherlock enters the new solution at his web site and the second hostage calls to inform them where he is, and that he's been released.
Later, Sherlock and John stop at a diner, and John points out that the bomber is playing a game with Sherlock. He wonders if it's Moriarty, and Sherlock admits it probably is. The pink phone rings with three pips and the photo of a woman. Sherlock has no idea who it is, but John says that it's a makeover TV queen, Connie Prince. Sherlock then gets a call from a blind woman, who is receiving messages from the bomber via an earpiece. The woman says that Sherlock has 12 hours, and the case is a "funny one." The bomber admits that he likes to watch Sherlock dance. After he hang sup, Sherlock watches on the telly as the newscasters announce that Connie Prince has died.
At the morgue, Sherlock and John examine the corpse. According to the houseboy, Raoul de Santos, Connie cut her hand in the garden and died of tetanus. Sherlock notices several cuts and punctures, and points out to John that Connie has a fresh wound on her hand, that occurred after she died. He sends John to get more information, and Lestrade wonders why the bomber pointed out Connie's death if she was murdered. He warns Sherlock that another hostage is at risk, and wonders what they're dealing with. Sherlock simply says they're dealing with something new.
As Sherlock goes over the case, he tries to determine the connection between the victims and the hostages. The blind woman comes back and reads a message from the bomber saying that Sherlock is enjoying it, and he only has three hours until she's killed. Sherlock then checks the websites, and discovers that Kenny hated her sister because she humiliated him regularly on her show.
John poses as a reporter and goes to see Connie's brother, Kenny. He admits that he doesn't know what he's going to do. As John talks to Kenny, he notices that the deceased had a cat, and its paws smell peculiar. He calls Sherlock and says that he's on to something, and tells him to pick up some stuff. Sherlock arrives, posing as a photographer, and John has him take several close-up photos of Kenny's hands. Once they're outside, John says that he smelled disinfectant on the cat's paws, and figures that Kenny used the claws to deliver the tetanus bacteria. Sherlock dismisses John's theory, saying that it's too clever for Kenny. The killer, Raoul, wanted revenge for Kenny's humiliation. The cat's claws have disinfectant on it because Raoul keeps a very clean house.
Back at Scotland Yard, Sherlock meets with Lestrade and explains that Connie died of botulinum toxin. Raoul was employed to give Connie facial injections of botox. He bought a surplus, bided his time, and then gave her an overdose. Sherlock admits that he knew it for several hours, but took advantage of the extra time to focus on the bomber rather than announce he'd solved the case. He posts the solution on his case and the blind woman calls him. She starts to describe the bomber's voice and the bomber sets off the explosives.
Later, Sherlock and John are back at Baker Street watching a newscast on the explosion. Sherlock realizes that the bomber usually stays above it all, but actually exposed himself by talking to the blind woman. John suggests that the bomber must arrange crimes, like Ian's disappearance and Connie's death. When Sherlock appears unconcerned about the blind woman's death, John snaps at him, but Sherlock insists that caring won't help and that John shouldn't make him out to be a hero. A new call comes in with two pips, and a photo of the Thames. Sherlock checks the tidal records to pinpoint it, and then calls Lestrade to report any strange occurrences in that stretch of the river.
The police eventually find a corpse on the shore and call John and Sherlock there. Sherlock wonders why the bomber hasn't been in touch, and then examines the body. He then declares that the Vermeer painting is a fake. When Lestrade admits he has no idea what he's talking about, Sherlock says that it's worth 30 million pounds, but it's a fake. Sherlock then explains that the clothing and varicose veins indicate the man is a security guard, working at a museum or art gallery. John determines that the man died of asphyxiation, but he didn't drown. Sherlock checks Interpol records and then tells them that the killer is the Golem, a famous assassin that squeezes the life out of his victims. There's a ticket, meaning the man worked at an art gallery or museum. The Hickman Gallery reported the disappearance of an attendant, Alex Woodbridge. Sherlock figures that Woodbridge discovered something that would stop the sale of the Vermeer, and someone hired the Golem to kill him.
As they take a cab to the Hickman Gallery, Sherlock stops off and pays a homeless woman 50 pounds, and slips her a note. As he leaves, he tells John that he's investing. When they arrive at the gallery, Sherlock sends John to investigate Woodbridge's flat. At the flat, John talks to the woman who shared the flat with Woodbridge. John discovers that Woodbridge was an amateur astronomer, but knew nothing about art. There's a message for Woodbridge on the answering machine, from a Professor Cairns. She tells Woodbridge that he was right, but Woodbridge's flatmate has no idea who Cairns is. As he goes, John gets another inquiry from Mycroft about the Bruce Partington plans.
Sherlock is disguised as a guard and admiring the Vermeer when Mrs. Wenceslas comes in and tells him to get back to work. He accuses her of hiring the Golem to eliminate Woodbridge, and insists that there's something wrong with the painting that proves it's a fake.
That night, Sherlock metes with John and gets his report. He then collects an address about the Vauxhill Arches from the homeless woman from earlier. Sherlock explains that he maintains a homeless network. They go to the location, where homeless people sleep, and spot the Golem, a tall bald figure. However, he gets in a car and escapes before they can catch him. However, John figures they can track down Professor Cairns.
Cairns works at a planetarium and is going through the footage, looking for a particular star. The Golem attacks her and starts to asphyxiate her. Sherlock and John arrive and the Golem attacks them from the shadows. In the confusion, he manages to escape.
Sherlock and John return to the gallery with Lestrade and accuses Wenceslas of hiring the Golem to protect her sale of the fake. The bomber calls to hear Sherlock's explanation, but wants to hear an actual explanation. He asks for time, and a child hostage starts counting down from 10. With seconds remaining, Sherlock realizes he's the only one who can solve it. He spots something, and then tells the bomber the solution is the Van Buren supernova. It only appeared in the sky in 1868, but it's in the painting from the 1640s. As Sherlock walks away, triumphant, Mycroft sends another message to John.
At Scotland Yard, Wenceslas says that she knew nothing about the other murders. All she wanted was the 30 million pounds. Wenceslas explains that she found an expert forger, and that someone took her idea to pass it off and developed it. She eventually made contact with certain people, and Sherlock gets her to admit that the name of her contact was Moriarty.
Exasperated, John finally goes to investigate West's death on the Battersea tracks. The trackman notes that there wasn't much blood on the tracks, despite the fact that West supposedly committed suicide. As the points close on a curve in the track, Sherlock arrives and explains that West was killed elsewhere and dumped there. They go to the flat of Joe Harrison, who Sherlock explains is Andrew West's prospective brother-in-law. Joe stole the memory stick and killed Andrew. Joe, a bike messenger, arrives, and John easily captures him. The killer explains that Andrew's death was an accident. Joe dealt drugs and got in over his head, and Andrew boasted about his job at his bachelor party, showing Joe the memory stick. Joe took it from Andrew when he was blind drunk. However, Andrew later realized what happened and came to confront Andrew. There was a fight and Andrew hit his head, smashing in his skull. He dumped Andrew out his window atop a passing train. When it hit the points at the curve in Battersea, it fell off onto the tracks. Joe gives them the memory stick, and Sherlock realizes they have to go back to the case, since there is still one pip left.
Back at Baker Street, Sherlock is watching telly and John can't help pointing out that Sherlock's lack of astronomical knowledge delayed his solution of the Vermeer case. Sherlock says that he returned the memory stick to Mycroft. John leaves to stay with Sarah, and Sherlock promises to get some food. However, once John leaves, Sherlock posts his solution to the Bruce-Partington plans on his website for the bomber, and tells him to meet at the pool at midnight.
At the pool, Sherlock calls out to Moriarty and invites him to collect the memory stick. Much to the detective's surprise, John steps out of the shadows. However, he reveals that Moriarty rigged him with explosives, and a sniper is ready to shoot at him. Moriarty steps out of the shadows: Jim, the IT guy. He boasts that he gave Sherlock his number, but he never called. As Moriarty approaches, he says that he gave Sherlock a glimpse into his world, where he works as a consulting criminal. No one ever gets to him, and he admits that Sherlock got the closest. However, Jim tells him that he has to back off.
When Sherlock offers Moriarty the memory stick, the master criminal tosses it into the water and says he could have got it anywhere. John grabs him and tries to use him as a hostage, but a sniper threatens to kill Sherlock and John releases Moriarty. Moriarty says that if Sherlock doesn't back off, he'll burn the heart out of him. When Sherlock notes that he's been told he doesn't have a heart, Moriarty says that he'd be true. As he prepares to leave, Sherlock asks what happens if he shoots him. Moriarty admits he would be surprised, but Sherlock wouldn't enjoy it for long. Sherlock doesn't shoot, and Moriarty walks away.
As soon as he's gone, Sherlock rips the coat and the explosives off of John, and confirms that Moriarty has left. He awkwardly thanks John for his sacrifice. The snipers draw beads on them, and Moriarty comes in and says that he's changed his mind, and that they can't be allowed to continue. John nods to Sherlock, who aims his gun first at Moriarty... and then the explosive coat on the floor. Moriarty realizes what he's considering, and smiles.