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huh, I didn't think of that. No, I would say make the player evil, but not necessarily the main monster. He should be the main threat to all of the "good" characters. At least as far as they know. 

So to answer more clearly : No, he does not have to be the main bad guy. But to all of the "good guys" he needs to appear as so--at least for most of the time.

Ah, so let's say, just for an example, you make a FNaF fangame where you play as William Afton (The man who caused everything) and you return to the Pizzeria and destroy the Animatronics (Good Guys) they ARE attacking you, but you are the villian? Because you made them like they are? You are facing your creations?

Oooh, I might actually make that, as a side project after I finish my main submission, I'll call it: SINS OF THE FATHER. Look forward to it!

The good people have to be good, in YOUR moral standards. So, they have to have good intentions, and  the player needs bad ones. I have played the game you are referencing, but don't remember how it goes XD

SPOILER ALERT:

Another thought: What if you were unkowingly helping the big bad? Like Cassie in FNaF Ruin? She unknowingly released the Mimic when she went to the Ruins of the Pizzaplex to save her friend, If not, why don't we add a challenge like that? Why not add:

"Make a game where you accidently help the villian"

I'd say that would be rather fun! :)