Pacifist - During the pacifist route, you'll only see Muffet at the spider bake sale. You won't fight her.
Neutral - During the Neutral route, you will fight her and have the choice of killing her or saring her. If spared, she will be found at the bake sale.
Genocide - During the Genocide route, you will only see her in her fight.
Muffet's wears an all-purple outfit. She'll hold glasses and a notebook. Upon defeat, her glasses will break.