For a long time River had thought that she was imaging it, that slumbering strength she felt in the heart of her brother, that it was something pulled out of her own trauma and psychosis. River may have been mentally traumatised but she was still a genius, and aware that her capacity to logically process mental input was impaired. Then she had realised she wasn't the only one who felt it, though perhaps she was the only one who really knew what she they were feeling.
She could see it in the way Inara looked at Simon like he was a puzzle to be solved. The way when Wash laughed with Simon it rang just a little hollow. The way Zoe and Jayne tracked Simon's every move with hands just slightly closer to their weapons than they needed to be. The way Kaylee sometimes looked at him with desperate sadness, like she knew there was something wrong. The way Shepard Book looked at him with a strange measuring look, like he was weighing Simon's soul.
And most of all in the way Mal faced Simon. Mal never treated Simon like he was a soft handed Core rich-boy, he faced him like an equal, like a man worth fighting. Mal probably didn't even realise he was doing it but River knew why, it was because somehow Mal felt that hidden feeling… that other… at the heart of Simon and knew that Simon was more than just the ship's doctor.
Or perhaps River was imagining it all. Perhaps she was just manifesting her own thoughts and feelings and projecting her madness onto the others. Perhaps Simon was nothing more than what he seemed to be, the only family she had left in the verse.
But deep in River's very soul a voice whispered, the same voice that whispered of planets she had never seen and beings which did not exist and horrors which had no name.
The voice whispered that one day Simon would wake up... that the mask he didn't even know he was wearing would vanish... and on that day he would stop being just a doctor and be the Doctor.