[tex]\huge\mathfrak\red {Answer:}[/tex]
Spoiler alert:
He thought the villain was Severus Snape.
But it was actually Quirrell.
[tex]\mathfrak\purple {Hope\: this\: helps\: you...}[/tex]
Answer:
Harry was suspicious that Professor Snape was the person trying to steal the Sorcerer's Stone, but it was actually Professor Quirrell (sorry, i'm not sure how to spell that!) and he was hiding Voldemort in his turban.