This is one of Tool's most amazing songs, and really sums up the entire theme of Aenima. This song is about growing, changing, and moving towards the next level of human evolution and conciousness. It's deeply rooted in Jungian theory.
Basically, it's believed that there are three levels of human evolution and each has it's form of conciousness. There's the 1st level with 44 chromosones. These are primitve people's like the aboriginies in Australia who do not percieve anything outside of themselves. They only see one large conciousness with no distinguishment between organisms. Then there's the second level with 46 chromosones. That is us. We are a chaotic disharmonic conciousness that is basically used as a stepping stone between the first and third levels. The third level is 48 chromosones. (Or 46 & 2, with 2 being the sex chromosones x & y). This is the higher level of conciousness. Our destination.
But this is where the Jungian theory comes in. It is believed that you can not reach this third level of evolution without first delving into yourself and basically cleansing your conciousness for the next jump. That's where the Shadow comes in. The shadow is basically everything about that is unseen that you are uncomfortable with or hate. This is also known as the Anima (hence the name of the CD).
The last part of the song sums all of this up...
"See my shadow changing,
Stretching up and over me
Soften this old armor
Hoping I can clear the way
By stepping through my shadow,
Coming out the other side
Step into the shadow
Forty six and two are just ahead of me"