The shit is information, and the fan a person or persons (often an employer or partner or someone in a position of seniority or superiority) to whom the information will be viewed as very bad news and also who is/are going to react immoderately and with no concern (or even some delight) as to whom the information then spreads.
This is an analogy for the worst possible development where concealment or deception have taken place and is a story in three parts: 1)The shit and the fan are seen as separate giving rise to nervousness of the awful consequences should they meet. 2)That moment arises, when time appears to stand still and the blades of the fan appear frozen for a split second. 3)There is an awful smell and a heck of a lot of clearing up to do.
The shit hit the fan when my mother returned home early to find my father trying on her best summer dress in front of the mirror.