John has seen the way Sherlock looks at him.
For being a genius and a master of disguise, Sherlock is horrible at this. He smiles crookedly whenever John compliments him; falls into a jealous sulk whenever John announces that he has a date (once he realises the date is not, in fact, with him); fails to hide his wistful gazes; brings home dangerous stakeouts and gory cold cases the way a cat might present a dead bird or mouse. Sherlock makes clumsy attempts at humanity, like microwaving a cup of tea for John ("It's simple chemistry! It's only water temperature! What difference does it make if the water is boiled or not?") and not insulting John's sartorial taste ("Those trousers are. . . adequate.") and playing songs that John likes on the violin, or thinks John would like ("Wait, but there's more--that was only the first movement!").
It's puzzling, therefore, that Sherlock hasn't made a move. After all, what Sherlock wants, he takes, whether it's crime scene evidence, a designer suit jacket, or--well, or John. Surely Sherlock knows that he already has John. All that's left is to make it official.
Maybe Sherlock's just shy. The man clearly doesn't have much experience with relationships. He probably just doesn't know how to make the first move.
Such is John's justification when he finally pins Sherlock up against the wall and kisses him. It's a soft and gentle gesture, the kiss equivalent of soothing noises and rubbing circles into someone's back. But Sherlock freezes in a way that makes John's stomach sink, and he pulls away, looks up, opens his mouth to apologise.
Sherlock says, "Please don't."
John has never heard Sherlock say please in a way that wasn't sarcastic, and that as much as anything else shuts him up with an audible click of his teeth. Sherlock takes that opportunity to slither out of John's arms and shut himself in his room.
For the next two days, John doesn't see any more of Sherlock than a coattail whisking around a corner, a strange stain on the kitchen table, or a terse text message: Experiment in jam jar. Do not consume. SH Sherlock's absence leaves John to putter in circles around the flat, absently straightening and disarranging and straightening again, making cups of tea for someone who isn't there, leaving the milk out and having to replace it. He's almost certain he read the signs correctly. Almost. Living with Sherlock has taught him that nothing is certain. Maybe he's bungled this.
Finally, he comes home one day to find Sherlock lying on the couch in his Thinking Pose, hands steepled under his chin. He sits bolt upright when John stumps in--his leg has begun paining him again, in an indistinct, half-hearted sort of way, as if it's undecided--and looks at John, but without making eye contact; his eyes focus on a point somewhere around John's kidneys. His hair is an even worse rat's nest than usual, and his shirt is half-untucked, his trousers less crisp than usual.
"I've come to a decision," he says unhappily, "and it's that I'm not leaving Baker Street. But if you insist, a compromise could be reached. Perhaps a timesh--"
"Wait." John holds up a hand. "Wait wait wait. Who's leaving? Why are you leaving?"
"I'm not." Sherlock scowls. "I found the place, and Mrs. Hudson was mine first."
"Mrs. Hudson is not yours, you can't own people," John says, deeply disturbed. "And what--am I leaving, then? May I know why?"
Sherlock's mouth twists; he looks somewhere between sucking on a lemon and having been told that the world will end in 36 hours. "Because it's not going to work."
John sits down in one of the armchairs before his legs give out on him. "What's not going to work?"
Sherlock waves a hand between them. "This. Us. Especially if you--" He wraps one of his hands into a fist and makes a frustrated grimace. He lays that fist on his knee and mutters something about beginning at the beginning. He fans out the fingers and drums them against his knee, once, and says, "I appear to be in love with you."
"Ah," says John.
Sherlock looks at the floor between his feet. The corners of his mouth remain tight. "I'm sorry."
"What?" says John.
"But the damage, once done, seems to be irreversible." Sherlock runs his other hand through his hair, to little effect. "The only solution, then, is separation. I'm sure you can see the necessity."
"I don't, actually," says John. "Back up. Explain to me why you're sorry?"
Sherlock looks at John, finally, and he looks sorry. He looks the most sorry John has ever seen him in their acquaintance, and Sherlock is never sorry. He wasn't sorry that time he made Molly Hooper cry or that time he insulted that victim's grieving mother or the many, many times he's disappointed John by being callous or selfish or too clever for his own good. The effect is devastating. "Because it's a terrible thing. Look at what comes out of love: ruin and murder. Love is the motivating factor in over 90% of the cases I take on."
"Good things come out of love too, you know." As soon as the words are out of his mouth it all becomes clear: Sherlock and his eerie brother who may or may not be the British government. Sherlock and "Mummy." Sherlock, for whom girls aren't his area, and boys aren't either, from the looks of it. God, even Mrs. Hudson, whose husband Sherlock ensured was executed for his crimes. Sherlock the consulting detective, for whom love is a poisoning victim with her face warped in fearsome agony; a suicide framed as a murder; a blackmail letter.
Sherlock is looking off to the side, and even the way the light hits his profile seems unhappy.
"No, really," John insists. "Love is--love isn't supposed to be like that. Love is growing old together, and celebrating birthdays together, and--"
"Love is like that," Sherlock snaps. "You can argue whether it's supposed to be, but the facts are facts." He rubs a tired hand over his face. "Now please go."
John is quite certain that if he leaves now, he will never see Sherlock again except from a distance, and maybe the occasional blurry photo in the newspaper. So he doesn't move. "No. Love is a two-way street, and you're not getting rid of me that easily."
"John," Sherlock says, and the earnest, beseeching face he turns on so easily for witnesses and neighbors and Mrs. Hudson is nothing compared to honest pleading. "Don't be stubborn. It's for both our--"
"No." John does move, then. He crosses the floor to sit next to Sherlock on the couch. Sherlock stops breathing. "I'm not going anywhere. I'm going to stay here and love you back, and there's nothing you can do about it."
Sherlock stares. "You're an idiot."
"Thanks," says John.
"Why on earth would you stay and risk everything for the chance to, to grow old together?" Sherlock demands. "I'm not a good person. I might murder someone for you someday. I might murder you, to keep you from leaving me."
"I've killed someone for you already," John points out.
Sherlock sits all the way back on the couch and remains staring at John. "You have," he says, softly.
"Yep," says John. "And I imagine I'll do it again."
Sherlock turns his head to gaze at the fireplace and the badly papered over happy face that once adorned the wall above it. "You--so that's it, then."
"Seems like it," says John. "Would you really murder someone for me?" Sherlock doesn't answer, so John leans over and kisses him. "Me too," he says, and Sherlock smiles.