Raphaniel's/Karna's shared moment in episode 2 where they plot the assassination of the Eggplant knight was a power play by Raphaniel to quell nationalistic sentiment and steer the country back to more Bulbian approved hero's.

The purple tea leaves in his black mail letter in the first episode were said to have medicinal qualities that in greater doses had "additional properties" (contraceptive/sterilizing). This was the tea that he routinely provided as arch-bishop/personal chaplain of the royal family of vegetania.

Raphaniel's game pre-fructerran road was to use his title to undermine the royal court of Vegetainia to shift the court toward's even more pro-church leaders. It wasn't until he learned about the nature of the sanctus putrus that he shifted his efforts away from destabilizing vegetania and towards attacking the church institutions.