Lyric discussion by polyethylenes1&2 

Cover art for Rotten Apples lyrics by Smashing Pumpkins, The

To me its all about a love he feels he could never have. Whether he feels he's undeserving, or the woman he loves is with somebody else doesn't matter... Love unrequited is love you never had so it doesn't make sense to me that it is a break up song. To me the lines "Dirty your face with longing and grace, God-given" seem to wrap it all up. The lines about "restless in my speach/ ruthless in my teach" and so on are all about how he loves her and he tries to show her through his actions, and his speach, but he's still afraid to just come out and tell her. Perhaps she is in a relationship with a friend and that's what he means by "When will I see her again/ the other side of friends/ the darkened clouds of death/ the empty-breathed desire" and also because the last lines: "life just fades away/ purity just begs" to me sort of show that he doesn't want to be the cause of the break up and "Dust to dust we're wired into sadness" seem to point out that he feels he has to wait, yet he also knows nothing will come of waiting... like his life has been programmed to be sad.