The main antagonist in 'Zayden Stormvoid' is definitely Commander Varen, but honestly, the more I re-read it, the less I feel he's a traditional villain. Yeah, he's the military leader opposing Zayden's rebellion, and he's ruthless in enforcing the Empire's will, but his chapters from the middle of the book onward show he's just following orders from a corrupt system he doesn't fully believe in anymore. He's trapped by duty and his own past failures.
What makes him compelling as an antagonist isn't some evil master plan, it's that clash of ideologies. Zayden wants to tear everything down for freedom, but Varen represents the flawed idea that order, even a bad one, is better than chaos. Their final confrontation in the rain outside the Citadel gates hits different because of that. You almost want him to have a redemption arc, but the book wisely avoids that, keeping him tragically committed to his path right to the end.