"in on" is not really a preposition at all, it is a phrase that means "involved in" , "had inside information about" , or "knows about" Example 1: If someone tells you a secret, then you are "in on" the secret. Example 2: If you know the news, then you are "in on" the news. You can rewrite the sentence as: "If Snape was involved in protecting the Stone, it must have been..." "If Snape had inside information about protecting the Stone, it must have been..."