As was the case in Rise of the Elgen, Dr. Hatch represents something greater than himself in the epic struggle of moral solidity against moral anarchy. With his philosophy of the inherent superiority of the strong over the weak, he argues that the strong (the electric children, i.e. the "eagles") have the right to assume power over the weak (everyone else, i.e. the "chickens") and use them in whatever ways they might wish. For example, in the first book of the series, Dr. Hatch has Taylor "reboot" a famous singer in the middle of her performance, causing her to forget the words. The act was purely for the enjoyment of the "eagles," serving no practical purpose. This type of cavalier exercise of power typifies his philosophy. He, being more amorally radical than the rest of Elgen, Inc., is the real enemy; he is a manifestation of the anti-moral spirit of Nietzsche and is therefore the mortal enemy of those who believe in a foundation for morality.
Michael and the Electroclan take a stand against this agent of wanton mayhem. By standing up to Hatch while keeping a solid ethical foundation, they represent traditional morality warring against the phenomenon of self-deification, which is essentially what Hatch is doing. Indeed, by making significant progress in destroying the fleet of the Elgen, our heroes make great strides in the war against moral anarchy. They must continue their valiant efforts in the next installment, when Hatch will attempt to use his new asset to achieve his ultimate vision of transcendence.
An interesting note; it's curious that Hatch refers to himself as the dragon in the metaphor taken from Revelation. In Nietzsche's allegory Thus Spake Zarathustra, he represents the obstacle of traditional morality as a great dragon called "Thou shalt." The lion must accept the challenge and slay the dragon of Thou Shalt in order to achieve transcendence. In this allegory, the electric children might come to represent the lion, and since Hatch is, by his own admission, the dragon (which is fitting, as he gives orders to the children and tells them what they shall do), the children could soon realize their superiority and slay Hatch in the same way that he tells them to slay all the other "chickens." In this way, Hatch might have made his own undoing (not dissimilar to Frankenstein, as Chairman Schema points out in the prologue).