Lyric discussion by The_Dragon_And_Emu 

Cover art for In My Body lyrics by Smashing Pumpkins, The

If this is referring to the Glass and the Machines of God story (which I read about here: http://www.billycorgan.it/modernfable.asp), then here's my interpretation of it:

"Hold silent / you were my violence stuck / in my life..."

I think this part is describing June, and how she was a dark reflection of himself.

"Just for the moment / and let me under you / so you can die..."

He felt like this was what she was basically saying to him, because she told him that "she never loved him at all".

"I was alive..."

He used to be alive when she was around.

"In my body / you'll never find me / you'll never pull me out... /...the lonely creatures scream"

He has been sad, withdrawn, and lonely, ever since her death.

"June's offcast / left hiding, I form the screams / burned alive..."

He imagines the horror of the car crash that June was in.

"Wasted sunsets / haunting my torment / right through my clothes..."

He felt like he wasted every single day being depressed about it and feeling betrayed. (By that, I mean in terms of how he realizes everything in the end of the story)