In the first episode, Vulgyre carpet bombs the Sidon flowers the Hoshikawas were cultivating on Planet Sidon. While it first appeared to be Zone being For the Evulz, the finale reveals the flowers to be Vulgyre's Kryptonite Factor. Thus it was more of a convert act of Pragmatic Villainy on Vulgyre's part.
Chevalier often sings a rendition of Kai Band's "Hero", a song about a casanova who desires of being his lover's hero. Just reading that description, you can easily see how it applies to Chevalier's personality and delusion of being a hero among Zone's ranks.
When Chevalier arrives to Earth, Empress Meadow shreds a tear of joy upon seeing him. At first, the male Zone members assume Meadow is fawning over Chevalier like Doldora and Zaza. But it takes a darker turn when Meadow is revealed to be mouthpiece for Vulgrye, who is male. Vulgyre was only happy to see Chevalier because of the death toll caused by the previous captain, which made him suitable Human Sacrifice for Vulgrye's use in his master plan to become a god.
Whenever Zone members try to enter a secret room they never seen before, a strange force knocks them away and Empress Meadow orders them to stop messing around and kill the Fivemen. It makes sense after Meadow is revealed to be hologram created by Vulgrye, he was attempting to keep key Zone members in dark of his existence from some being accidentally digested after stumbling into his stomach. But once Vulgyre is forced to reveal himself, he no longer needed to concern himself with the Zone members' well being.
In the first episode, when Zone arrives at earth, the Hoshikawa siblings and their students safely evacuate the school before Zone completely destroy it. But there aren't that many students with the siblings, and the siblings can't be the only teachers at the school, not to mention that there isn't a school principal in sight. Did the other students and school staff...?
After being demoted, Garoa ends up being a janitor on Vulgrye. The strange thing is that there is no custodian force on a ship as big as Vulgrye. Prior to Vulgrye is being revealed to be a living being, Garoa twice nearly entered a secret room that turns out to be Vulgrye's stomach chamber. Considering that, it does hint that previous janitors and low-ranking Zone members below anyone's radar might have ended up there to be digested off-screen.
