It seems as though the ending is going to be pretty predictable. I'm guessing it's one of those stories where the villain is really good at heart, and while his creations/henchmen start going of the deep end, he works to stop them from doing whatever massively evil deed they plotted behind his back. At the end, Archer and he will be looking at each other across viewscreens, as things start blowing up around Soong and he makes some poignant quote. Then again, I could be way off.