Sherlock and John already know the Doctor. Sherlock met him before he met John, and he had helped him, and vice-versa, on numerous cases. The Doctor is just visiting them (by accident).
It's just a scene out of a much bigger story which I will never get around to writing, so it may seem a bit dis-jointed. But I really like the idea, because not many people write it like this, so just bear with me.
Sherlock was alone in the flat. John and the Doctor had gone out to buy groceries. At least, that's what John thought would happen. Unfortunately, (for John at least), John didn't know the Doctor well enough to know going shopping with him was a bad idea. Just going out anywhere was a bad idea with the Doctor. Especially in his eleventh reincarnation! He was like a highly intelligent four-year-old. In fact, sometimes he thought he was a four-year-old child!
Anyway, John and the Doctor had gone out to buy groceries (as well as some sweets, cat toys, flour, and whatever else caught the Doctors attention). That meant that there was no one to talk to, no one to annoy, no one to invade the privacy of, and no one to ignore. That, for him, was the bedrock of boredom. At least normal people were silly enough to be worth deducing.
But no, he had the flat to himself. He had to deduce the desk, the pictures, the umbrella that he had stolen from Mycroft. How utterly insignificant and dull those deductions were.
Desk: a gift from one of Mrs Hudson's friends, 4 years old, numerous coffee and tea mugs dumped carelessly on its battered surface. It was handmade, not shabbily, but not high-quality either. Boring.
Skull Picture: one of his, given to him by an old client some years ago. Not British made, probably German, but certainly not from China, too expensive. Marks on the top left corner, and the bottom left corner, from some explosive experiment most probably. Not worth re-selling, but he wouldn't want to sell it anyway. Not sure why.
Mycroft's stolen Umbrella: made early 1950's, British, classic wooden curved handle, high quality, expensive. Looked after well, no scuffs, or rips, even though Mycroft has had it for some 7 years. Perfect blackmail material, but best not mentioned too soon.
His eyes gleamed at the opportunity of getting the upper hand on his nosey brother. But, he felt his heart sink when he realised he would need his brothers resources at some point, and should keep it until then. Unfortunately, that meant no blackmailing today. He would only regret it if he did.
He sighed. There was nothing to do in his boring, boring flat. He detested boredom, but there was nothing to do. He would have to just lie on the sofa and wait for John and the Doctor to come back. He closed his eyes and put his hands in the 'thinking position', trying to guess what useless oddities the Doctor would have brought. It was pointless, as he had neither the data nor the will power to make anything more than an educated guess, but it occupied the mind, for a short while at least.
Sherlock jumped out of the sofa suddenly. There was something wrong. The air didn't feel right, he could sense something that shouldn't be there, but he couldn't explain how or what it was. As if on cue, a whooshing, grating noise pierced the silence of the flat, and an unexplainable wind (for it had no source or viable exit) swirled around the flat, making the end of his blue dressing gown billow around his feet. And then he could see the faint outline of a blue rectangle, fazing in and out of existence in the middle of his now untidy flat.
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