Disclaimer: I don't own BBC Sherlock.
Three years.
That's how long it's been.
John was surprised that it's been three years.
Because frankly, it felt like every day just blended into the next, making time just seem like a giant ball rather than a linear concept to him.
He tried living with Harry after it happened because the flat was just an empty shell without him. When he was with Sherlock, he felt so safe. Like he was home. But nonetheless, he decided to move back into the flat. Mrs. Hudson always stopped by for tea every evening so that they could talk about the happenings in their lives and around town. There was the unspoken agreement of not touching on the topic of Sherlock, but that lasted for all of two months. They decided that it was better to reminisce on the good times that they had with him and celebrate his life. But other than Mrs. Hudson, John only briefly talked about Sherlock with others. They didn't know him like he did, as cliché as that sounded. They only saw the high-functioning sociopathic consulting detective, not the 6-year-old genius consulting detective that John adored.
He kept himself busy by sorting through all of Sherlock's things, taking the time to reading his case files, reflecting on the memories in each of them. Eventually, he made his way throughout the flat, cleaning the place up and packing his belongings in boxes. He couldn't bear to get rid of them. It would have felt like getting rid of him as a whole. It was bad enough that he wasn't there, but to dispose of the only things connecting them to each other…he didn't think his heart could take it. He even went through the library of books that Sherlock had, laughing at the various stories involving adventures out at sea. Mycroft was right: He really wanted to be a pirate. But he went through and read all the books, letting his imagination take him to the highest places and away from reality, if only for a moment.
It was about 6 months before John mustered up the courage to go into Sherlock's room. The only other time he was in there was when Sherlock was drugged by The Woman and he had to throw him back onto the bed. As soon as he stepped through the doorway, the tears came. It felt like he was a lingering presence in the room, but John knew it was a lie. He shakily inhaled, the sobs wracking his body as he took in Sherlock's scent. They never hugged or anything, but they were attached at the hip. Sherlock's scent was committed to his memory: Slightly musky and almost of a microbiology lab. It was odd, but it was comforting. He brought his laptop into the room, pulled up his iTunes and hit shuffle. Ben Gibbard's voice faded into the background as John let all of their adventures weave in and out of his mind while he organized Sherlock's belongings. There really wasn't much to be organized since Sherlock had everything in its own section, but he did it anyway because he wanted to know everything about him. He snorted at the sock index and the time that he messed with it, just for fun. The next day, it was back in order. John never touched it again because he learned that to mess with Sherlock's things was like trying to drill into his brain the idea that the solar system existed: trouble.
The room wasn't particularly messy to begin with, but he supposed it was just an excuse to feel enveloped by his best friend. He was never one for frivolous things and his room echoed it. Probably because all of his stuff was in the kitchen anyway. Just a periodic table and a judo certificate adorned his wall. His desk had his laptop, a notepad and a tin can filled with pens and pencils next to it. It was only when it was dinner time that he left the room. The rest of the evening, he went through his closet, noting the purple shirt. He would never admit it out loud, but he always thought Sherlock looked the best in that shirt. In fact, he bet that Sherlock knew because he remembered that he wore that shirt the day that he started showering John with compliments in the cemetery. He debated about sleeping in Sherlock's room for a while and just decided to go with it. The bed was nice and all, the sheets cool against his skin, but it wasn't enough. The only thing that could make it better was if there two people in the bed, instead of one.
It took about eight months before John came back to work at the hospital. Sarah understood he needed to be alone with his thoughts the moment she saw it on the news and she received his email. All she said was that he could come back when he was ready. When he finally did, she tried not to show her surprise at his change in demeanor. He was still kind, patient, had a tremendous work ethic, and was warm with his patients. Something was off though. His eyes said volumes of what he wouldn't say out loud. They were empty, as if someone turned off the spark. She never asked him because she already knew the answer. It killed her to see him to continue going about his business, being an emptier version of the man he was before Sherlock entered his life. So she did what she could, be a supportive friend. She was patient with him, just making small talk during breaks. It was around the fall when John started talking more, which led to the routine of getting coffee on Friday afternoons after work in a little hole-in-the-wall café in Brixton. They stayed there until dark, chatting about everything. They came to view each other as siblings, always open with each other. She felt like she had done a good service when she saw him laugh out loud at the comedian at the café one night. There was a sense of unbridled joy radiating from him in that moment, and she wished she could have captured it because this was the John Watson that everyone longed to see. They weren't going to be able to see him for a while, so they had to wait.
Lestrade consulted him sometimes on some of the more minor cases, knowing that John was still wary. It was strange calling him up to ask if he would like to help out because there was always that void when he walked onto the scene. He wasn't Sherlock, but Lestrade figured that with him being his best friend, maybe some of that intellectual prowess rubbed off on him. John surprised him by doing a fairly decent job. If Sherlock were there, he would of course point out everything that John missed, which wouldn't be that much because John could deduce in his own right, but he would have done it with a tender smile on his face. Everyone saw how deep their relationship was. There was only one title that seemed to fit those two because everything else made it seem superficial. They were soul mates, whether they liked it or not. He couldn't see how they wouldn't like it though. Even though they drove each other up the wall like an old married couple, at the end of the day, they were inseparable and meant to be in each other's lives.
Sarah wasn't the only one who hated seeing John in pain, recovering by millimeters. Molly was the one to help orchestrate Sherlock's death. She had to deal with holding in the secret that she was the only to know that he was alive. Still, she maintained her usual chipper demeanor. But she couldn't help but think back to when they had to formulate it.
He suggested at first that he should take some of the Rhododendron ponticum and Grayanotoxin that would make his pulse stop temporarily because he knew that John would be the first to check. They both realized that this wouldn't work because of several things. The time it would take for him to get out of the truck that one of the people from the homeless network would be driving wouldn't be enough because John would be sprinting to the scene. There wasn't enough time for the drug to take effect. Plus, in order to look dead, it would involve fake blood. Lots of it. It should be easy; just pouring it all over his hair and lying on the pavement. However, he knew that John would see right through it. She noticed that while he was working out the plan, his eyes, while they were wild, still held this sadness. Her deduction proved to be correct: He was sad when he thought John couldn't see him. Now that he knew that John thought he would never be able to see him again, he didn't even bother to try and hide it. She loved Sherlock even though he treated her like crap, but seeing him this broken about having to leave the one he loved behind, she would do anything to help him. If she was anything to him, she was going to be the one to save both of them in the end.
Molly's plan was brilliant, really. She found a corpse that looked like him and dressed it up, slapped on a wig and doused it in blood, and waited for her cue. Thanks to the flat that was in front of Bart's, Sherlock landed into the very padded truck bed without being seen actually falling into it. One of the people from the network on their bike collided with John, giving the group of nurses and doctors the chance to create the scene, and to disorient him. Sherlock specifically said she didn't count when talking to Moriarty because he needed her and he needed her to be safe. As soon as he landed in the truck, she planted the body and sprinted away. From the shadows, she saw John walking to the scene, still wobbly. She swore she could hear his heart shattering as soon as he saw the body and she had to step back, her sobbing becoming uncontrollable. She received a text from an unknown number that said, "Take care of him. And thank you for everything, Molly." Taking a moment to compose herself, she returned to the mortuary to await "Sherlock", putting on her game face for John.
Everyone was still trying to find their way through life without him. Even Donovan and Anderson attended the funeral, her head buried in his shoulder and the tears streaming down her face. She knew she made a mess of things, but she had no idea that it would lead to this. Nothing could have prepared her for how his death shook London to its core. Sherlock had embedded himself in each of their lives and to have him ripped out…leaving wounds was an understatement. They left the funeral silent, both contemplating how they treated him like he was a freak. But he wasn't a freak; he was the most brilliant man they had ever met. After that day, they were especially tactful with John. They experienced what military John was capable of after they gave Sherlock a particularly hard time. That was something they never wanted to go through again.
It took approximately John 15 months before he finally felt like he could be okay without him. Like his heart wasn't going to break every time he passed Angelo's, or passed by a hat shop with a deerstalker in the window, or when he saw a tall brunette in a swishy coat walk by him. Then he went back a couple of steps. He had to muster up the courage he had as a solider, being able to walk away from battle with his composure intact after seeing his friends die on the battlefield. It seemed like he had let his heart rule his head for so long, it occurred to him that this was a battle that he was just never going to win.