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John was just walking home when he heard footsteps. Before he could turn around to see who they belonged to he’s been dragged into an alley and pinned to the wall. Before he could do anything, his arms and legs were being expertly bound by sharp copper wire. Indignantly, “Must you use that? Couldn’t you use something normal, like zip ties?” Moriarty than started speaking in a sing-song voice, “Now where would the fun be in that? We’re going to play a little game. I want to see if Sherlock still wants his pet after I’ve ruined you.”
The next thing John hears is a zipper being undone and than blinding, white pain. He can’t tell if he’s screaming or not, everything is gone and there is just pain, unending pain. Vaguely he can feel the copper wire ripping at his skin and the sounds of Moriaty breathing heavily.
And than the sounds are gone, and there are footsteps. John doesn’t know how long it takes him to come back to himself. How long it takes him to untangle his hands and than his legs from the copper wire. How bad the cuts from the wire are. How long it takes him to stand up and pull his pants back on without tears welling up.
He limps home, somehow. Sherlock is in his room, playing the violin and sulking. Normally that would worry him, but not now. All John wants to do is go to the bathroom and clean himself up before Sherlock notices.
Unfortunately for John, Sherlock heard his loud, clumsy footsteps and heavy breathing while he was still on the staircase. As he passes Sherlock’s room to go the bathroom the door opens and Sherlock gasps. That’s all it takes for John to fall on to the still considering Sherlock and begin sobbing.
Everything after that is a blur. John vaguely notices when Sherlock realizes what’s happening, and tentatively begins to stroke his back and murmur something reassuring, or as close as it gets with Sherlock. He vaguely feels himself being gently guided to the bathroom, Sherlock carefully cataloguing and cleaning his wounds. The gentle way Sherlock handles him, as if he was piece of fine china.
The next thing he’s properly aware of is Sherlock speaking. He’s staring intently at John’s wrists, and murmuring over and over “This wasn’t supposed to happen.” “It should have been me, this wasn’t supposed to happen.” John starts crying again, which sets Sherlock off.
Eventually they calm down enough to finish caring for John, for John to explain what happened to Sherlock. For Sherlock to tell John over and over that he isn’t ruined, that Sherlock will always love and cherish him as his friend and companion, For John to make it clear that he doesn’t want anyone else to know about this, that he doesn’t want to report it, that he can’t handle everything that comes with reporting a rape. For Sherlock to slip outside of John’s earshot and ring Mycroft anyway.