The Seer and the Story's Theme
The Seer is intended to serve as an embodiment of the main characters' struggles. During the course of the narrative, the point is made and belabored that the inherent nature of most video game characters/sprites is to kill, maim, and murder thoughtlessly. The entire aim of a sprite civilization is to control and suppress those urges, with varying degrees of success. Now take The Seer; like the sprites, it's a construct of human design, and like the sprites, it was designed to destroy everything. At first, it seems as if it's defied its nature and taken on a new purpose, lending itself subtly to the theme the comic espouses: self-determinism wins out over programming.
Instead, The Seer turns out to be The Man Behind the Man. His seeming shift is motivated only by a desire to destroy more than computers. In short, his nature is what inspires him toward self-determinism, and though he defies human interference like the sprites, he is still bound by his programming. Ultimate destruction is what he lives for, and all he does is a means to that nihilistic end. Where he has chosen to embrace his programmed nature, the other characters defy theirs, and defeating him is a final, symbolic act of victory on their parts, resolving the questions the comic put forth.
In this way, the comic stresses that one's inherent nature is not nearly as important as the decisions one makes.