Lyric discussion by salmonpudding 

Cover art for Pneuma lyrics by Tool

Pneuma definition: (in Stoic thought) the vital spirit, soul, or creative force of a person. I don't think this song has anything to do with Christianity or religion at all for that matter. I think it's another one of those simply spiritual Carl Jung/Ayahuasca-inspired songs. It's about the collective consciousness. How we all come from the same source. We're all just a piece of a great collective consciousness that is divvied up into different beings. Similar theme to "Parabola." We're spirits bound to flesh, held in mortal bodies. For now... We get so entrenched in this life, this 'reality', we need to wake up and remember our true origins, our true being. Remember what it was like before we were groomed into conformity, into this reality. Like being a very very young child. An almost impossible task unless through meditation or psychedelics.

EDIT: I'm not saying this song is "about drugs." Just saying it's about concepts a lot of people have difficulty grasping because they've never experienced an ego death or other mode of perceiving reality- experiences that often require mind-altering substances like DMT, or serious meditation to achieve. Experiences at least some of the guys in TOOL have undoubtedly had.

this reality = "this dream."

Similar concepts in the song "Third Eye" as well.