The first episode of "Sherlock" Season 3, "The Empty Hearse," opens with Anderson theory of how Sherlock cheated death. Anderson's theory includes funny-looking Sherlock mask that was put on Moriarty's face, fall-arrest rope, and Sherlock and Molly Cooper's kiss. According to him, it was Moriarty who was pushed off the roof, wearing Sherlock's mask. Sherlock jumped off the roof, wearing a harness rope. He broke into one of the windows of the hospital, jumped inside, kissed Molly and escaped death. Inspector Lestrade rubbishes Anderson's latest theory and tells him that it is his guilt that is making-him come-up with such absurd theories, as he often said that Sherlock is a fraud. Lestrade says that Sherlock is definitely dead. Anderson screams that he believes in Sherlock. Also, after two years, Moriarty's truth has finally surfaced and Sherlock's name has been cleared.
John visits Sherlock's grave. He is sporting a moustache. However this time, he is not alone as a woman joins him. The next scene is that of a jungle in Siberia. A man is captured and is tied-up. The captured man escapes the torture by correctly deducing the events in his captor's life and warning him about his cheating wife. There is another man who is watching the interrogation between the captured man and the captor. Once the captor leaves to check on his wife, the man sitting in the dark is revealed as Mycroft. He goes to the captured man and says, "There is an underground terrorist network active in London. And, a massive attack is imminent. Sorry, but the holidays are over. ... Back to Baker Street, Sherlock Holmes!
Watson returns to 221B. Ms Hudson is angry that Watson did not keep in touch and hadn't called for months. It has been a difficult, grieving time for both Watson and Ms Hudson. Watson finally is moving on. He informs Ms Hudson that he has someone in his life and he is all set to propose. Ms Hudson thinks that a man is going to take Sherlock's special place. Watson has to spell it out that he is not gay and he is dating a woman.
Sherlock informs his brother that it took him two years to dismantle Moriarty's network. Mycroft tells him how he infiltrated the camp of the Siberian criminals to save Sherlock and learned Siberian language in a couple of hours. Also, Mycroft tells him about the terrorist attack and wants Sherlock to stop it. Sherlock wants to know about Watson. Mycroft tells him that things have changed and he hadn't communicated with Watson. However, Sherlock correctly guesses that despite no communication, Mycroft must have kept a watch on Watson. Mycroft gives Sherlock Watson's file and also informs him about the location where he could meet Watson in the evening. He also warns him that his presence will not be welcomed. Sherlock takes a look at Watson's latest photo and does not like Watson's moustache. According to him, it makes Watson look ancient.
At a posh restaurant, Sherlock sees Watson and takes the disguise of a French waiter to surprise his friend. Watson is there to propose to his lady love, Mary. However, the proposal scene is interrupted when Sherlock finally manages to get the attention of Watson. Sherlock sums-up his appearance in a short version: "not dead." Once Watson is able to completely absorb the shock that his friend is indeed alive, he punches Sherlock.
Watson is not interested in knowing how Sherlock faked his own death. He is more interested in knowing why he did that. Sherlock says, it is because Moriarty had to be stopped and it was all part of Mycroft's plan. Watson demands to know who all knew. He is furious to know that Mycroft, Molly and 25 more people knew about Sherlock being alive. He beats-up Sherlock and refuses to join him to stop the terrorist attack. Sherlock asks Watson only one question whether he is going to keep the moustache. He also points out that Mary does not actually like the moustache and the look on Mary's face confirms that. Mary tells Sherlock that she will talk Watson out and later tells Watson, she likes Sherlock.
Sherlock is back at 221B Baker Street and Ms Hudson screams seeing him. Sherlock meets Lestrade, too. Lestrade hugs him, relieved and happy that Sherlock is not dead. Mycroft visits Sherlock and after a round of brotherly banter, the elder brother reminds Sherlock about the seriousness of the terrorist attack.
As Watson refuses to join Sherlock, Molly is enlisted as the assistant of Sherlock Holmes. While Sherlock passes time solving mundane cases and Molly taking notes, Watson looks bored to death in his physician avatar. Watson has shaved-off his moustache, which according to him has nothing to do with Sherlock disliking it.
Molly and Sherlock visit a man. An employee of the railway system, the man shows Sherlock a tape of a bizarre happening. A man entered an empty compartment at one station but did not get out at another. He simply disappeared in thin air despite there being no way he could have got down at any point between the two stations.
Sherlock tells Molly about a fish and chips shop in the corner. Molly demands to know what it is all about. It is Sherlock's way of saying thanks for helping him. He tells her that Moriarty made a mistake and slipped out because the one person (Molly) he (Moriarty) thought didn't matter to him (Sherlock) is the one person who mattered to him the most. Molly is engaged and Sherlock gives her a little kiss and they move in different directions.
Mary rushes in at Baker Street to inform Sherlock that Watson's life is in danger. Watson has been kidnapped. Mary is receiving cryptic messages on her cell phone. Sherlock figures out that there is not much time left to save Watson. The two take a wild motorbike ride to reach the place where Watson is being held captive inside a pile of wood, which a person lights-up with the intention to burn Watson alive. Sherlock manages to save Watson.
Later, Watson visits Sherlock and is surprised to see Sherlock's ordinary parents. Talking about the ordinariness of his parents, Sherlock says that it's the cross he has to bear. Watson comes to know that Sherlock's parents also knew about him being alive.
Watson and Sherlock have an incomplete reconciliation. Sherlock again watches the video of the tube. The man who disappeared is Lord Moran. Sherlock realises that it is not just the man who disappeared but one whole compartment disappeared, as well. The man working at the railway system informs Sherlock and Watson about a completed station that was closed even before it opened. Sherlock and Watson rush to that station as the attack is all set to happen the same day. Sherlock is not interested in taking the help of the police as he finds them bothersome. Sherlock correctly figures out that the terrorist attack aims to blow-up the House of Parliament. Sherlock and Watson find the missing compartment. When they enter it, they realise that the whole hollow compartment is a bomb. Lord Moran activates the bomb, sitting in his hotel room. Sherlock panics as he does not know how to defuse the bomb. He wants Watson to leave the compartment but it is too late to do anything.
As the end is near for both, Sherlock wants Watson to forgive him. Watson thinks it is another of Sherlock's trick and wants Sherlock to use his stored data in his brain to defuse the bomb. Sherlock feigns helplessness and Watson finally forgives him and closes his eyes, waiting for the detonation. When nothing happens, Watson opens his eyes to see a smiling Sherlock. Sherlock had to simply switch off a switch to defuse the bomb. There is no going back on forgiving Sherlock for Watson.
Watson tells Sherlock how he had gone to his grave and had spoken to him, wishing for a miracle and wanting him to stop being dead. Sherlock reveals to him that he was there when he spoke at the grave. The two friends have finally patched-up. Lord Moran is arrested.
Sherlock reveals to Anderson how he cheated death. The meeting of Sherlock and Moriarty on the roof of the hospital was as a result of a long-term plan set in motion by Mycroft. It was a plan to dismantle the extensive criminal network of Moriarty. Mycroft and Sherlock had laid a trap for Moriarty and they had allowed him to tarnish the image of Sherlock.
At the time, Sherlock ready to take the jump had asked Watson to keep looking at him. It was to stop him from watching the working of 'Save Sherlock' act. Mycroft had planned a clean escape for Sherlock, with no one getting a hint of Sherlock being alive. There were a group of people posing as doctors, nurses, biker and onlookers. A huge air bag was placed to cushion the fall of Sherlock. Once Sherlock safely landed, the bag was taken away, thanks to the ambulance station. The corpse of one of Moriarty's men -- who resembled Sherlock and had scared the kidnapped children of a boarding school -- was pushed down by Molly from a window.
This corpse was taken away from the spot for a while to deceive Watson. Sherlock took the place of the corpse and a squash ball was used to stop his pulse, temporarily. Hit by the biker on the street, shocked and dizzy, Watson had fainted after he checked the pulse of Sherlock, thinking his best friend is dead.
Anderson is disappointed to hear the way Sherlock faked his own death. He refuses to buy Sherlock's explanation, as he realises that he is the last person to whom Sherlock would reveal the truth.
At 221B, Sherlock, Watson, Mary, Ms Hudson, Lestrade are having a little get together. It is revealed that Watson has got engaged to Mary. Molly joins them with her boyfriend. Molly's boyfriend is a look-alike of Sherlock.
Sherlock and Watson walk out of the door to meet the waiting press. Before stepping out, Sherlock wears his hat. "It is time to go and be Sherlock Holmes."
The final scene is of a man watching the video of Sherlock rescuing Watson from the bonfire. The man's face is not revealed but the eyes tell that it is our villain of this season.
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