And John remains blissfully unaware that The Doctor visited Sherlock years ago and gave him the skull. It was a skull he’d discovered in a ruined church, a thousand years in the future. He couldn’t re-bury it in the grave it came from, because that was completely destroyed, so he took it and gave it to a young Sherlock.
‘This will keep you company until you meet him,’ the Doctor said with a smile.
Sherlock took the skull and immediately began examining it. ‘Who is it? Or rather, who was it?’
‘It’s all that’s left of an old man who lived a good life and became the most important person in yours’.
The Doctor never gave him the name he so desperately wanted, but as soon as he met John Watson on that fateful day in St. Bart’s, Sherlock knew.
After John ran off to see to Mrs. Hudson, before Molly walked through the lab on her way home, the familiar sound of the TARDIS landing interrupted Sherlock’s frantic puzzling. As the Doctor stepped out into St. Bart’s Hospital, his grave expression caused Sherlock’s rising plea for help to die in his throat.
“I’m so, so sorry,” said the Doctor.
“You could not-?”
“No. This, what’s about to happen, it’s a fixed point in time. You have to die.”
“So then why are you here?” scoffed Sherlock. “Come to grant a condemned man’s last… Oh.”
“Yes,” replied the Doctor calmly. “Anywhere in space and time. Is there anything you want to see?”
Sherlock considered. “I’d like to see John again,” he said at last. “Please, Doctor?”
The Doctor didn’t appear surprised by this request. “Of course,” he answered. “But you must understand, you can’t talk to him. He can’t see you.”
“Yes,” Sherlock appeared resigned. “I know.”
Sherlock stepped out of the TARDIS into a familiar graveyard. The Doctor joined him, and indicated the corner of the crypt they were standing next to. “Make sure you stay out of sight,” was all he said.
Sherlock cautiously peered around the corner, and spotted John and Mrs. Hudson, a little ways off, standing in front of a fresh grave. His grave, he realized. Almost as soon as he saw them, Mrs. Hudson started walking away towards a waiting car, leaving John looking lost by the grave. John started talking, and Sherlock realized that he was close enough to listen.
He’d never imagined John cared this much. He wanted so badly to run to him, grab him, cry “It’s okay, John, I’m not dead, I’m here!” but he couldn’t. As the broken soldier strode away, Sherlock found he couldn’t even bring himself to cry.
He returned to where the Doctor waited, pity filling his eyes. “Thank you, Doctor,” Sherlock said, voice even as ever. “I’m ready to return now.”
In his heart, Sherlock resolved to talk to John again before he died, to say whatever he must to prevent what he’d just seen. He would convince John that Sherlock Holmes, Consulting Detective had been no more than a con and that John, like the rest, had been played.
Surely then John could be happy without him.