A/N: Alright, so this takes place after Sherlock comes back from the fall, but I can't really see a roll for Mary in this, so I'm just operating on the idea that she either broke up with John, or didn't exist to begin with. This story is going to focus on Sherlock and John's friendship, and the aftermath of the fall on the both of them. Enjoy!
Sherlock sat in his chair plucking at his violin strings staring into nothingness. They didn't currently have a case, but thoughts still filled his mind. They were those little, persistent thoughts that you could manage to ignore most of the time if you had something to distract you. Donovan and Anderson's words echoed throughout his brain as he tried to figure out exactly what they meant when they called him a freak. He knew it wasn't a good thing, but what exactly was the definition of 'freak'? Sherlock knew that it made him feel not good, but he never understood why. Why does this word affect him more than others? Why does it have a sort of negative ring to it?
People had called him 'Freak' for as long as he could remember, yet he never did figure out what it meant. He wondered about so many things like that, yet could never bring himself to ask anyone. They were foolish things, he supposed, things that the answer of which should come to him naturally. But they didn't.
He hadn't been bored much lately, these thoughts taking precedence in his mind. He was content to attempt to puzzle these things out, trying to find answers himself. This was easier said than done.
John sat in his chair reading the paper, looking up periodically expecting Sherlock to say something, or declare his boredom to the world by shooting the wall, or spray painting another yellow smiley face on it. Instead, Sherlock just stared past John at the wall, not looking at anything in particular. Sherlock had been nearly mute for several days now, saying no more than good morning and good night, only answering an 1/8 of the time that John spoke to him. This was starting to worry John now. Sherlock wasn't begging Lestrade for a new case, and wasn't doing any experiments. His violin playing was limited to an idle plucking of the strings. He hadn't eaten much in the past bit, only the orange slices and quartered hard boiled eggs John occasionally lined up on the sofa or chair's armrest for him to find. Even so, Sherlock had probably only eaten about two boiled eggs and one orange in the past five days. He had only rarely taken a sip or two of the water glasses John left here and there throughout the flat, but every one of them was at least 3/4 full, so John knew Sherlock was probably also significantly dehydrated. John knew he hadn't been sleeping either.
"What are you thinking about?" John asked.
The quiet strumming stopped momentarily and Sherlock rested his fingers over the strings to stop the vibrations.
"Stuff." He said, glancing up at John momentarily before beginning to pluck the strings again.
John hadn't expected an answer, but was pleased that Sherlock had at least registered that he had spoken.
"What sort of stuff?" John asked.
"Just stuff," Sherlock sighed. "Nothing important." He stood up and returned the instrument to it's case. He returned to his seat and sat again, this time staring off down and to his left, his head only partially following his gaze.
"You've been thinking about that not important stuff for five days now, you know that, right?" John asked.
"Has it been that long?" Sherlock said passively, "Five days?"
"Hasn't been for you, you haven't slept." John answered.
Sherlock just hummed his acknowledgement.
"Are you feeling alright?" John said, leaning forward and resting a hand on the detective's forehead. Sherlock just hummed.
"Sherlock, I'm serious." John said. "Are you alright?" John reached out to check Sherlock's pulse, and it was then that Sherlock snapped out of his head. Sherlock swatted John's hands away, but it was a delayed reaction, as he had looked at them a moment first.
"Fine, John." Sherlock said. "I told you. I'm just thinking..."
John hadn't had time to get a full reading on Sherlock's pulse, but had felt it for long enough to know that it was significantly lower than normal. While it wasn't unusual for Sherlock's pulse to read low when he had just been in his mind palace, these numbers were concerning. John had in this time realized that Sherlock's respiratory rate was slow as well. Sherlock was breathing only once or twice per minute. It was showing too, as his oxygen deprived skin had taken on a blue tinge. Sherlock had gone back into his mind palace, and John knew it would only get worse. John stood up and got in front of Sherlock and just shook him. John knew he would probably end up getting yelled at, but he didn't care.
"Breathe, you idiot!" John said. After a moment Sherlock gasped. For a few seconds he was breathing hard, and John could see the color returning to his skin, his body no longer deprived of the oxygen it so badly needed.
"Why did you shake me?" Sherlock asked.
"You weren't breathing!" John said.
"Is that proper medical protocol?"
"It is for you Sherlock Holmes!" John said. "So tell me, why did you want to go and stop breathing?!"
"Must have forgotten." Sherlock shrugged, "Happens sometimes."
"You forgot to-" John shook his head. "How in the world can you forget to breathe?! It's not something that you think about doing, it's automatic!"
"I get sucked into my mind palace, and all my brain space goes to thinking, not breathing." Sherlock explained. "It's quite simple really."
"How did you survive without me?" John sighed.
"Unhappily, I can assure you." Sherlock said under his breath. He paused for a moment, "And I definitely don't want to have to again. My senses missed your presence."
John froze. That was about as close to sentiment as he had ever heard from Sherlock.
"You missed me?"
"I said my senses missed your presence, and I suppose that would be the same thing as missing you, so yes, of course." Sherlock said. "Why would you think I didn't?"
"I don't know, maybe because you didn't tell me you were alive for three years!" John said, then clamped his mouth shut. That had come out with much more bitterness than he had intended. He already knew that Sherlock felt bad about it. Sherlock glanced away. He opened his mouth to speak, then shut it.
"I'm sorry." Sherlock said. "I didn't want to make you feel that way."
"I know." John said, as he shifted positions. "And I've forgiven you. It still hurts though."
Sherlock nodded and adjusted positions himself.
"Did you wish I was with you?" John asked. "While you were gone, I mean." He knew it was a foolish question, Sherlock Holmes would never admit to that much sentiment, but John hoped Sherlock would give him a straight answer.
"Depends." Sherlock answered.
"On what?"
"On the time and place." Sherlock said. "Sometimes yes, sometimes no."
"Why did it change back and forth?"
"I wanted to be with you, here." Sherlock said. "Not you with me, there."
"You never have told me," John commented, "What happened to you while you were gone?"
"I..." Sherlock hesitated, then changed the subject. "Chinese or Angelo's for lunch today?"
It took John a moment to process the change in conversation.
"Angelo's" John said, "And you can tell me what happened while we eat."
"John..." Sherlock sighed.
"This is what friends do, Sherlock." John said. "They tell each other things."
"Ugh! That's the whole point, John!" Sherlock said, standing up from his chair quickly. "I'm not sure you'll want to be my friend afterwards!"
Sherlock then realized what he had said, and how a burst of emotion had been released from himself. He reddened slightly before exiting the flat quickly.
"Sherlock wait-" John said. The door slammed.
It was then that John had time to process Sherlock's wording.
I'm not sure you'll want to be my friend afterwards! Sherlock had done something bad then, John reasoned, something he was ashamed of.
John had forgiven Sherlock for faking his death for three years, what could Sherlock have possibly done that was so wrong he didn't think John would forgive him?
A/N: Wow! A lot happened in this... I hope you like it, and I hope you keep reading it to see where it goes. There will be more, so onward read! Reviews please!