IMO..

"I've got a catacomb
with fur covered styrofoam"

This probably speaks of an imaginary place he dreams of when he can't sleep.

"time isn't here again
wasted thoughts that could've been
now we can devise our plan"

Time stops when you are in a deep depressed mood.
Dreams and/or memories of things that could have been or continued lingers in his mind.
Troubled and pressured, he struggles to devise a plan.

"daylight won't find us here"

So true when you're stuck in darkness.

"i've got a catacomb
with flags that flew fifty years ago
let sleep overcome your mind"

This is a big guess. Something about his youth that troubles him? Something he heard or learned about history? Something "got lost" fifty years ago? Rest can help a troubled, clouded, worried mind.

"God isn't safe again
molests trees and chops down men
se we must revise our plan"

Failure sounds like a positive band so I assume that this sounds deeper than it may seem.
Peace, goodness, etc. is in trouble. Man does not follow what is good from bad therefore `God isn't safe, again' and ends up doing what was mentioned. Revise our plan? More care?

I see it as a story about a patient in an asylum or psyche ward.

The apples symbolize both life and blood. Gone from her eyes, and bleeding out to the rug.

"...everything you've left behind" could mean freedom. I'm not too sure about this... since she's trying to "free" the patients from their "sickness," maybe she's "free" as a ghost so she "can't touch freedom" or cannot touch the subject of the patients being or getting "free" from their conditions.

In my imagination, the nurse is probably doing bad things to the patient. That's why the patient made her "apples" spill on the ground. :)