John began to notice that something strange was going on.
The strange thing being that every apple he brought into the house somehow disappeared before he had a chance to eat them.
(They were hidden until he has no choice but to investigate the strange smell and toss out the rotten fruit or experiment viciously on.)
This goes on for several months until he found a dozen apples dipped in acid and left in the kitchen sink.
He stood before his flatmate/boyfriend/whatever Sherlock considered them to be ("Boyfriend is too juvenile for what our relationship is.") and demanded "What do you have against apples?"
Sherlock muttered, "'An apple a day keeps the doctor away', John. Three years without you is more than enough for one lifetime."
John rolled his eyes in exasperation and plopped himself beside the frowning detective. "Didn't think you were one to believe a silly rhyme."
"You can never be too cautious."
"Right you are," John reached up and placed a feather light kiss on Sherlock's cheek. "But I'm not going anywhere, so leave my apples alone."
Sherlock rolled his eyes, but conceded, "I'll leave the apples alone."
He was rewarded with another kiss.
(And that is the story of why apples are not experimented on in the flat called 221 B.)