Tool - Pneuma Lyrics Meaning

Pneuma is "spirit", the song is essentially about becoming enlightened to some degree, letting go of ego and grudges that ("drag you down like a stone"-The Grudge).
Connection with spirit ("we are all one mind" -reflection)

"Wake up remember
We are born of one breath, one word
We are all one spark, sun becoming"
That this is an illusion, we are limited(one foot nailed down) by this existence and our bodies(This flesh)
We are bound to become spirit