According to KM, it’s connected to the theme of “The Mirror” with betrayal and disillusionment being the main theme. There also seems to be religious symbolism in the lyrics.
Lie includes themes of betrayal, with both points of view, about not wanting to give up on somebody who is a lost cause, but then realizing that they’re worthless in the end. A deceitful, hurtful person who is willing to do all that they can to milk another person for personal gain. Portnoy has claimed that Lie, much like all of Moore’s lyrics from Awake, it is really about Moore’s desire to leave the band.
Lie was originally part of “Puppies on Acid” in its demo form. After being split into two songs, this second part took on the name “Kittens on Crack” in it’s demo form.