The Doctor's life is very busy, and very dangerous, and to bring a filly along would be irresponsible, or perhaps even reprehensible! Occasionally, though, a quiet moment crops up - a brief period of peace during which he's not attracting danger like a magnet attracts iron filings. Whenever such a moment arises, there are only two ponies on his mind.
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This story just came out of the blue today, I sat down in a fit of procrastination, aiming to write a (mostly) unrelated short story about Pinkie Pie, but this ended up getting typed instead.