John had a fascination with Sherlock's eyes. He felt as though he could stare at them for hours and still not know why he found them so captivating. From day one, those eyes had warranted his attention and time had not lessened it.
Perhaps it was the unique color—a grey so pale that it seemed almost crystalline. It was their light color that made them so open to reflection, making them seem blue and sometimes even green.
It also could have been the fact that his eyes were often the only place that emotion could be read on his face. Even there, one had to look deeply to see it. So many people didn't take the time to search out that hidden emotion, thinking the man to be a machine that felt nothing. John knew differently.
Then there was the interesting way that his eyes grew so unfocused when he was thinking, and yet so piercing when he was reading you. It almost seemed as if he could strip away everything to study your soul.
And when Sherlock focused his eyes on John, the doctor couldn't help but shiver at having his soul bared before the detective. Who else could claim that they had held the full attention of Sherlock Holmes without being a part of a puzzle that he was trying to put together? There was always a question in Sherlock's eyes when he studied John, but it took a while before John figured out what it was.
Sherlock couldn't deduce why John was still there; why he still put up with him. And despite not knowing why, he was thankful.
Sherlock's eye conveyed the mind of the man behind them to the world. They allowed John to see who Sherlock was behind the mask.