Update: When the Black Omen rises, two green gates appear. One on the 65,000,000 BC world map and one on the 600 AD world map. I checked the 65,000,000 one out, it's a Reptite cave, with a pseudo Guardia forest and a marsh. When you defeat all the monsters in the forest the Reptites in the cave part come out of hiding and will keep asking you favors. The second one was to retrieve a golden hammer or whatever. I also briefly checked the 600 AD one, but it seems to be the same concept as the 65,000,000 one. It's not the same place, but it looks identical and has the same concept. Anyway, I found this part too boring to check it out further. I don't think it has anything to do whatsoever with canon. Just a little extra to gain experience, items, and money. I found only one thing intriguing: There's also a mountain part, but at the very beginning a dark colored Nu is blocking it, so it's impossible to say what's there for now.
I'll probably complete the game in a couple of hours.