Well this is how I took this song, apologies if someone thought of this already and it's a repost

This song seems to be outlining the uses of a specific material. Fire, or a stone, specifically.

They way one uses an object, is determined by their will, being Good-Will, or Bad-Will. As to the the first person, or the first user of the material, that uses it in a productive way, simply uses material to create a home-like environment. He represents good-will.

The second person, representing bad-will, uses the material to inflict harm onto others for personal gain. Misusing what could clearly be used for better.

Relate this to real life and what we know about Tool:

Tool has always been for the progression on the mind through utilization of substances

What I believe that they're trying to say is that substances branded as dangerous, are actually materials in the same way, twisted by the will of the person utilizing them, positively, or negatively, and that there is no use in fearing a substance, but the will of the user is the real thing to fear.