Admittedly, I know very little about drugs. I do get the feeling this song deals largely with drugs and depression/mental illness. Mary is the drug itself, the silence comes from its ability to quiet her mind. I think I've heard somewhere that either heroin or LSD is sometimes called Mary. Let's dissect it...

She's really tempted by the drug's promise of happiness at the beginning. So she digs in. I'm not sure what the next part means. I think it has something to do with the feeling that she needs the drug in order to avoid suicide or hurting herself. She's craved the drug, the beautiful release it gives her. She personifies Mary, wanting to be all that the drug gives her. The steady confusion is the noise in her head, coupled with the decision to or not to use drugs. "You're looking at fear" could imply a number of things--fear of a bad trip, fear of suicide, fear of addiction. But Mary always "walks out in a hurry", never quieting the narrator's mind enough. The narrator descibes another ambiguous scene, checking her head in Mary's windowpane. It could possibly mean testing her willpower vs. the drug. I think it has more to do with a mirror she cuts the drugs on, or maybe even a bad reaction that leads her to putting her head through glass. She can't get her mind of of her feelings of worthlessness, she can't bear to suffer anymore. She thinks that her drug will make it all okay, that if she can be high, she'll forget her pain. She keeps on trembling in fear, seeking consolation. Seeking Mary.