Complete Monster: From Series IV, Dark Koutei, in the form of a giant eye, is the main, and worst, villain of the entire series. One thousand years ago, he and his army attempted to take over a solar system before being locked away by the Big Good; another thousand years later he reemerges. He is a truly Bad Boss: instead of just berating or even firing his minions, he locks them up in strange, inescapable domes, doomed to float around in space for all eternity. There's also the matter of how he procured his son: by kidnapping a child and corrupting him. Koutei manages to be the most despicable villain in Bakugaiden without really trying.
Ho Yay: Dr Graybon and Dr Shadow's reactions to see each other after years include dovey eyes, dancing and a Bishie Sparkle. Possibly invoked for laughs.
Viewer Gender Confusion: Dokudandy's tall, thin body and effeminate mannerisms make him seem like a girl for first-time viewers.