Symbolism, Imagery, Allegory
Worms get a bad rap. They do wonders for the soil, but because they help stuff decompose in the ground, they get associated with dead bodies.
Got it. But what do worms have to do with the story?
Let's set this up. A new patient named Lucia shows up at the hospital and tells the other patients how D ward isn't as bad as other hospitals she's been in. According to Lucia, living in D ward makes the patients scared, and that's because of what she calls "the little maybe" (13.53). The other patients understand this "little maybe"—it's the hope of maybe one day getting well and being part of the world.
Hope is tricky. Hope can keep you going, but if, like Deborah, you've been stuck between worlds for a long time and don't know how to interact like a normal person...well, then hope can be scary, because it means you have to give up all you know in order to change.
The thought of living outside the hospital and giving up the symptoms of her illness (like Yr and all its gods) makes Deborah start seeing a dark cloud settling above her, and worms start falling out of it.
Worms are traditional symbols of death they're the ones who show up to feast on our dead flesh and turn us into compost. Not pretty, but true.
Deborah thinks about worms when she thinks of getter better and leaving the hospital, because the very promise of sanity and normalcy will mean the death of Yr and therefore a death of part of herself. She's a teenager, and she's been living with Yr since she was five. It's very much a part of her that she's afraid to lose.
We'd be seeing worms, too, probably, if we had to give up everything we ever knew.