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Of course John knew. First of all, he wasn’t a complete idiot, no matter what Sherlock Holmes occasionally said about him. Second of all, he was a man of faith. No, not religious faith, just… faith. Faith in the universe, faith in what he believes, God notwithstanding. Faith in Sherlock.
Sherlock Holmes was alive. John had known that was the case from the very second he saw Sherlock’s ‘dead’ body lying on the pavement. He had also been running with the detective long enough that he knew when it was time to play along and lie his arse off. He was a surprisingly good actor, when called upon, if he did say so himself.
He played along then, and in the days to come. He played along through Mrs. Hudson’s tears. Through the haunted look in Anderson’s eyes. Through the haggard grief that was oh-so evident on Lestrade’s face. He never has to try to fool Mycroft, though, for which he is grateful. His masquerade wouldn’t hold up under the scrutiny of a Holmes.
He played along right through Sherlock’s funeral. He knew his friend had a reason for whatever it was he had done. Oh, of course, he had his moments of doubt. Faith in anything can never be entirely unshakeable, and he had been shaken. He had felt so sure that any moment Sherlock would show up in their sitting room, or on a street corner, or - really, anything, anywhere, any time. He hadn’t. John’s worst moment of doubt came the day he and Mrs. Hudson visited Sherlock’s grave.
“Please,” John says, fists clenched, back ramrod straight. “There’s just one more thing, one more miracle, Sherlock, for me. Don’t be…” His voice wavers, “Dead. Would you do that just for me? Just stop it. Stop this.”
He has his moment, then reels everything back inside. He has faith. He does.
The next day, his blog hit counter clicks one number higher. Almost every day after that, in fact, it gains a single number. If a day is missed - and these are days John spends mindlessly refreshing the page over and over again - a day or two later, the counter changes to accommodate for those missed days.
It’s certainly Sherlock - he was so sure that the stuck counter was a clue, and now it’s his clue for John. It’s his message for John. He is out there, and he is safe.
What surprises John, really, in the end, is just how long Sherlock is gone. Two years is more than enough time for a man with a temper like John’s to generate enough rage at so many things to fuel a jet engine.
He is angry at not knowing what the point of this is. He is angry at being left behind. He is angry that his best friend only communicates with him through the hit counter on his fucking blog. He is angry at the surety that the reason Sherlock misses updating the counter occasionally is because he is probably doing something dangerous, and John is also angry at his own helplessness to protect the other man. Most of all, he is angry that he is so fucking angry.
He has faith in Sherlock Holmes, and sometimes he feels that this faith should be unquestioning. Other times, he feels that maybe he’s better off, and that he’s a lunatic for having faith at all.
Still, he plays along. He can only assume that this is what Sherlock is expecting him to do - and despite the fact that he is full to the brim with rage at all times, he still doesn’t want to let the man down.
He goes to work because he wants something to do. He goes to therapy, because people are expecting it, and keep suggesting it. He masters a pained expression to use around people that are expecting him to be heartbroken. After a while it becomes a little more real - he is heartbroken - just not for the reason people believe.
He meets Mary, and against his better judgement, she finds her way into his life, and into his heart. He loves her. She is clever, funny, and beautiful, and he tells her about his life, with Sherlock and without. She doesn’t speak much about her past, but he can understand that sometimes one doesn’t want to revisit certain things.
He puts off truly moving on, though, because he hasn’t stopped waiting. The counter clicks slowly, and steady up. 2500, 2525, 2547 - and then it stops. One day, not quite two years since the day Sherlock fell from Bart’s, the counter stops changing. At first, he experiences his normal level of worry. Sherlock is out there, doing something that means he can’t update the counter, and John always worries it is something dangerous. A week goes by, then two, then three. He is beside himself, and can’t tell anyone why, can’t show it.
Finally, he cracks and sends a short text to Mycroft: ‘Everything okay?’
The reply is unhelpful: ‘I am not sure to what you are referring. MH’
Does Mycroft know? John honestly isn’t sure. He hasn’t seen the man since before Sherlock’s death. He didn’t even come to the funeral. He can’t push it.
Another week, and one day John wakes up with something cracked inside his chest. That’s it. He’s been fake mourning Sherlock for two years, and now he’s having to mourn him for real. The cracked thing in him is tired, and sore, and he…. gives up.
He buys the engagement ring that afternoon, and reserves a table for that evening. He’ll ask Mary for her hand, and he will move on with his life. That will be that.
When he sees Sherlock standing there with that ridiculous drawn on moustache, the cracked feeling simultaneously seals back up, and ruptures completely. His actions at that point are out of his control, but he retains enough faith, enough belief, and enough love for Sherlock that he never says anything that would betray the secret that he knew the man was alive.
Years later, he and Sherlock and Rosie are in the sitting room. Rosie is on the couch reading a book, and the two men are seated at the fireplace. It’s Christmas morning, and everyone is contented in that way that only Christmas morning can bring.
“John,” Sherlock says, suddenly, locking eyes with him. “You knew, yes? The whole time?”
Even after all this time, John knows that he is talking about the fall. “Yeah, I did,” he tells the detective. “Didn’t make it much easier, though.”
His faith had taken a plummet there at the end, certainly, but it didn’t matter now. He believes in Sherlock Holmes.
