This is just my version of what happens after The Fall, before it comes out on TV. Enjoy!
When John woke up, Mrs. Hudson had already gone. He leaned forward out of the uncomfortable hospital waiting room seat and peeked side to side, looking for an indication of where she had gone. Lestrade had left before, on the search for Moriarty.
Strange of Mrs. Hudson not to leave a note.
He would have assumed that she had simply stepped out for a drink from the vending machines on the floor below, if he hadn't heard a familiar voice answering him.
"I had the Detective Inspector take your landlady home." Mycroft Holmes was sitting opposite John. There was no telling how long he'd been there. The two men were alone in the waiting room.
"Has the doctor come out yet?" John asked, still groggy.
"It...is finished." This answer jolted John awake, and he stood.
"Can I see him?" He was already walking towards the door. Mycroft stood after him.
"I am afraid it is too late for that, Doctor Watson."
John's eyes narrowed. He looked down at his watch. 4am. "Oh, of course. I'll just wait 'till morning, then."
Mycroft frowned. He leaned down to pick up a coat from the seat next to him. John recognized it as Sherlock's second best. Mycroft pulled a piece of paper from it's pocket. "I had Mrs. Hudson send it back with Lestrade. He always kept items of importance in here." He held the folded paper out to John, who took it, bewildered. "It is addressed to you."
John looked down at the letter in his hand. He cleared his throat. "Have you read it?" Mycroft shook his head.
Unlike you, Mycroft.
"Are you going to read it now?"
"Anything in it he could tell me himself in the morning."
"Doctor Watson...I'm afraid that's not possible."
John switched his route and made for the exit. "I think I might go home, check on Mrs. Hudson. I'll come back at visiting hours-"
"John." It was the use of his first name that stopped the Doctor. He could not look at Mycroft, though. "You know what I am about to say."
"No, I don't. You'll have to tell me."
"Sherlock...is dead."
And immediately, John grinned. He turned around.
Good plan, Holmes. Who knows who could be watching the hospital.
"Yes. Yes, absolutely. So...shall I go to the morgue, then? To identify the body?"
Mycroft's frown grew more intense. "That won't be necessary. I've already done so."
"Well, then, where has the body been moved to?"
"It hasn't. It's to be cremated in the morning."
John had stopped smiling by now. "Mycroft...?" No answer. "Mycroft." Sherlock's brother had never looked older to John than in that moment. "He's not dead. Not really."
"It pains me to inform you that he...is."
"Yeah, but I think we both know that's not quite true, don't, we?" John whispered, moving in close. Mycroft's face answered him. "You really believe this, don't you? You really think-?" And then, in his hand, a clue.
Smarty-pants bastard.
John sat in the nearest seat, unfolding Sherlock's note. He read it once, and then again. Minutes passed. He looked up at Mycroft. "No...it's in here. I know it's in here. I'm...I'm looking right it. I'm just...not seeing."
Not observing.
"Doctor Watson, I'm so sorry."
"I want to see him." John stood up.
"No, John, you don't." Again, first name. It wasn't that John couldn't see Sherlock, it was that he couldn't want to.
"You're sure it's him?"
"Positive."
"You were...thorough."
"Completely."
"Do you even care?" John regretted his words immediately after spouting them. He would have apologized, but Mycroft had already begun to respond.
"Doctor Watson, I raised my brother from the time I was in college and he was barely a young man entering middle school. So, trust me when I tell you: I do care."
I'm so sorry, Mycroft.
He should have said it out loud.
And Mycroft left John there, standing in disbelief, alone in the waiting room. And Sherlock Holmes was dead.