Considering this is Maynard, he's more than likely the only one that knows the "true" meaning of the song (unless he talks about it in an "interview" I missed.) He typically leaves his audience to make of it as they wish, hence his primary band name Tool (use the music as a tool for yourself.)
The general story of the song is about a patient in and out of a manic mental state and his delusional fascination in his caring nurse. The music is atmospheric, calm and meditative giving off the feeling of fantasy and imagination. Ultimately, the song is very dark with strong metaphoric value Maynard accomplishes so well.
Within the first verse, the patient fancies the integrate patterns of the rug. "Say hello, to the rugs topography." He assaults the nurse and pushes her face to the floor to visualize how she and the rug look together. "It holds quite a lot of interest with your face down on it."
After doing this, medical staff sedate him and take him away, "Say hello to the shrinking in your head." When the sedative starts taking effect, the patient is fighting against it and is soon unconscious. "You can't see it, but you know it's there so don't neglect it."
The chorus focuses on his misconceived love for the nurse and his love for medicine. "I'm taking her home with me," is his determination to have or take the uniform wearing nurse. "All dressed in white." "She's got everything I need, Pharmacy keys," she has the key to making him feel good (love or medication?)
As nurses are typically kind and friendly at heart, the patient notices these general nurse-like acts of care and kindness as love. He's so wrapped up in his delusional love, he doesn't notice the nurses behavior with other patients. He believes he is receiving special treatment. "She acts just like a nurse with all the other guys."
Within the verse in question, the patient is in a manic imaginary state."Say hello to the apples on the ground" is in reference to the nurses red pool of blood (roughly the size of an apple.) He see's the nurse as an "apple of my eye." She is deceased or unconscious as the red "apple" pools of blood accumulate from her nose onto the rug. "They were once in your eyes, but you sneezed them out while sleeping." The nurse has lost her life including everything she was or had (including the patient,) "Say hello to everything you've left behind." The death of the nurse is beautiful and important as she can no longer reach for it. " It's even more a part of your life now that you can't touch it."
"I'm taking her home with me, all dressed in white" He snaps from his fantasy to see the nurse bringing him love (or medication?) "She's got everything I need"
The multiple vocal layers within the 3rd chorus indicates an alternate reality the patient is experiencing. (Voices in my head.)
The final verse is the very same as the first, "Say hello to the rugs topography." The patient receives medication from the nurse and the love cycle continues.