It wasn't that the plants and earth itself were entirely made of dark mana. It was more so that they were so greatly full of it that they had changed appearance to match the dark and light mana. It wasn't even in complete opposition. It came together to make a perfect balance.
"This is perfect." Onyx spoke out to make it clear that just existing here would be beneficial to the dual affinity both he and every young serpent had had.
The fact that the manas were balanced and flowing calmly meant that the idea Onyx had about a naturally occurring dual affinity rune had to be true. His entire being was resonating with this space and that couldn't just be the dungeon. Instead, it had to be what was made within the dungeon.
They all knew that the dungeon needed the pure light and dark manas from the naturally occurring runes. Therefore, those manas had to go somewhere before being sent back in to the world when the dungeon was open to the world.
