"The Napoleon of Crime" — Jim Moriarty — never rested. Near-simultaneous major incidents occurred at the Tower of London, the Bank of England, and HMP London, yet for Moriarty, this was merely the opening move in his little game with Sherlock. Moriarty's goal was to turn Sherlock into a false hero and utterly destroy his reputation. Though incredible, seeds of doubt were sown and took root after this series of events. Most people came to believe Sherlock's exploits were entirely fabricated, a hoax.
The final confrontation took place on the rooftop of a high-rise. Moriarty demanded that Sherlock jump to his death; otherwise, pre-positioned assassins would immediately kill Sherlock's three most important friends: John, Mrs. Hudson, and Lestrade. Sherlock reasoned that as long as Moriarty was alive, his friends were safe. To Sherlock's shock, the utterly deranged Moriarty immediately shot himself in the head, solely to force Sherlock to jump.
John arrived at the street below just as Sherlock prepared to jump. Sherlock called John. Perhaps to prevent his friends from feeling guilty, Sherlock finally confessed to John that he was a fraud and asked him to publicize the truth. But John, believing in Sherlock's innocence, begged him to stop. At that moment, the snipers took aim. For the sake of his friends, Sherlock ultimately fell before John's eyes, his last words being, "Goodbye, John." This scene later connects back to the opening where John is seeing a therapist due to Sherlock's death.
In the epilogue, John and Mrs. Hudson visit Sherlock's grave, reminiscing about his infuriating habits: the knife marks on the table, the noise, gunshots at 1:30 AM, the damned specimens in the fridge, corpses stored with the food, and various fights... As he speaks, John's voice breaks. At the graveside, John says:
"...you were … the best man … the most human … human being that I've ever known, and no-one will ever convince me that you told me a lie… I was so alone … and I owe you so much … But, please, there's just one more thing, one more thing, one more miracle, Sherlock, for me, don't be … dead … just stop it…"
Tears stream down John's face. His sincere grief and lonely figure are watched by Sherlock, standing unseen in the shadows. The film ultimately ends with Sherlock turning and walking away...