A Study In Bat!John

It was two years after 'The Reichenbach Fall'. John Watson had lost his best friend that day. Sherlock was more than a best friend to John. After loosing him it made John go into a state of depression. The years were like a sharp knife slowly being pushed into his chest. Afghanistan was a mere phase comparing to the loss he was suffering.
John would visit Sherlock's grave almost everyday, but he couldn't let himself go back to 221B Baker Street. Going there was far too much to bear for the man. The flat smelled only of Sherlock. Sherlock's items still scattered about as if he never left the flat. John removed all his personal items into the flat he was sharing with himself. He had become so lonely. The only thing left in 221B was his chair and a few boxes. Inside the boxes were nothing more than a few extra jumpers John had kept. Sherlock would always make the comment, "your jumpers are ridiculous".
As the days grew darker so did John's fate.
One night John took the pistol he carried with him, and he placed the gun to his head. He pulled the trigger.
John Watson was dead.

It was indeed a shame, for Sherlock was to arrive and surprise him.
Sherlock had not been dead, but had faked his death to save his beloved John Watson.
"I think I'll surprise him. Go to 221B Baker Street and jump out of a cake." Sherlock suggested half jokingly.
"You can't; he isn't there anymore" Mycroft said in a dull tone.
"Not there anymore? Well where is he?" Sherlock questioned his brother.
"Dead." Mycroft stated.
"John's..dead?" Sherlock said almost as a whisper repeating Mycroft's dreaded words. Sherlock's mind began to race in all ways possible. He couldn't believe John was dead. How? John certainly wouldn't have let someone murder him, and suicide was out of the question. Ah-ha!
"You're smiling? Is it funny to you that your only 'friend' is dead?" Mycroft questioned.
"I'm not foolish, Mycroft. It's all a big bluff to deceive me into thinking John is dead. He's planning on surprising me, isn't it?" Sherlock said rather smugly.
"No, Sherlock. John Hamish Watson is dead." Mycroft said and handed Sherlock several magazines and news papers that showed pictures of the detective's colleague whom killed himself; took his own life.
Sherlock's eyes scanned the papers. "Papers don't prove anything. My death was all over them." Sherlock protesting not wanting this to be true.
"I suppose you could visit his grave-" Mycroft said before being cut off by his younger brother.
"Grave? Graves don't prove any evidence at all to ones death! I even have a gravestone!" Sherlock said having a bit of a hissy.
"Now, let me finish, brother. John Watson's body was handed over to science for a DNA collection. He was a war vet that committed suicide. It was only best to donate his body there. They wanted to 'find out a reason', but we all knew it was because of you. Maybe he thought he could see you in the afterlife." Mycroft suggested shrugging a bit having all his support on the umbrella he carried.
"Don't be foolish Mycroft, he wouldn't be able to see me in the afterlife." Sherlock scoffed can't helping but to prove his brother wrong.
Reality. It hit him hard. He had to restrain himself from crying in front of Mycroft. "Excuse me." Sherlock said and left.
In the cabbie Sherlock let it go. His eyes leaked. His mind palace was crashing. "211B Baker Street." Sherlock said in his baritone voice trying to let no emotion escape his voice.
He walked inside, and Mrs Hudson screamed. Her voice rang in his aching head. He silenced her with a hug and kept walking. Her voice of constant questions, lectures, and stories of what he missed was drowned out of his head. He stopped and stared at John's chair.
Mrs. Hudson seemed to have gotten the memo and nodded. "I'm sorry, darling." She said and stopped herself from mentioning any more about John. Then turned around, and she left.
Sherlock explored the flat gently touching his possessions such as his violin and skull. Sherlock went up to John's room and opened up one of the boxes full of jumpers. Sherlock lifted it to his nose and smelled it. John. He sunk his face into it.

This depressive state long lasted a couple months. Lesterade even tried to cheer him up with cases once he found out he was back. Sherlock discarded them. First, they are extremely easy. All simple murders if you actually take the time to look at it. Second, John wouldn't be there. John. How could he go on another case without John at his side. Chasing down a murderer. Hating what Sally would call him. 'Freak'. John would always compliment him with 'brilliant' and 'amazing' now that was gone. All gone.