John was asked by a friend for help and went to a gathering spot for young drug users to search for his friend's addicted son. Unexpectedly, he encountered Sherlock there. For the sake of a case, Sherlock had relapsed into drug use, which infuriated Mycroft. However, Sherlock insisted that his drug use was solely for investigative purposes.
John brought Sherlock back to Baker Street and was surprised to find that Sherlock had a girlfriend—Janine, the bridesmaid from his wedding. But John soon discovered that Sherlock was dating Janine only to gain access to her workplace for his investigation. Sherlock pretended to propose marriage to infiltrate the office of Charles Augustus Magnussen. John accompanied him.
Just as Sherlock found evidence that Magnussen was being blackmailed, the blackmailer turned around—it was John's new wife, Mary. To protect her identity, Mary shot Sherlock. Using all his knowledge, Sherlock managed to protect his vital organs and survived the severe injury.
It was revealed that Mary had been a government agent who went into hiding after growing tired of her dangerous life and later married John. John learned the truth about Mary from Sherlock after he regained consciousness. Ultimately, John chose to forgive Mary, especially since Sherlock did not reveal that she was the shooter.
Magnussen possessed Mary's files and used them for blackmail; he also held compromising information on various Western nations, posing a significant threat even to Mycroft. To protect Mary, Sherlock and John confronted Magnussen again. However, Magnussen was a master criminal with a phenomenal memory. Sherlock initially believed there was a secret archive storing the blackmail materials, but eventually realized the information existed only in Magnussen's mind.
To protect Mary's identity, safeguard Mycroft, and national interests, Sherlock made the drastic decision to shoot and kill Magnussen in front of the police, leading to his own arrest. To protect his brother, Mycroft arranged for Sherlock to be sent overseas to Eastern Europe on a six-month covert mission.
John and Mary saw Sherlock off. Sherlock never told John that Mary was the one who shot him. After Sherlock's departure, a video of Moriarty was broadcast across the nation's television signals, suggesting that Moriarty had not died in the fall from the rooftop—raising profound questions. To uncover the truth about Moriarty's possible survival, Sherlock was recalled to London by Mycroft to resolve the crisis.