After Maria, Toby, and their crew trick Malvolio into thinking Olivia loves him and wants him to behave foolishly, they lock him in a dark room and hold him prisoner. (They get away with it because Malvolio's behavior leads Olivia to believe he's insane and possessed by demons.) Once Malvolio's bound in the dark room, Feste pretends the room is as bright as day and says Malvolio's "mad" or "ignorant" if he believes the room is dark. Darkness, then, becomes synonymous with Malvolio's supposed insanity.
Of course, the dark room is only temporary. Malvolio is eventually released and let out into the "light," where he learns the truth about the phony letter and Olivia's true feelings. It's important to note that Malvolio's revelation comes immediately after Viola and Sebastian come face to face and Viola reveals her identity. This seems to invite the audience to see Viola's "Cesario" disguise as a kind of darkness that covers the truth throughout the play.