In the "film" scene (disc 3) Laguna sees lunatic Pandora taking flight...Yet the direction is to the east, rather than to the west (the location of the crater).

If we analyse the plot; Laguna investigates Esthars secret operation and after escaping becomes sick. After recovery from illness, he conveniently finds work right next to the very military excavation he was forced to escape from!
Additionally, it seems a bit odd that a film maker would choose "area 51" as a place to film a parody of St George (slaying of the dragon).... would you not agree Big D?


As you can see, I am convinced that there are practically no tangible explanations for the crater! The crater is truly on the same level as childhood myths, it inspires a certain discomforting revelation... sometimes it is better to ask the right questions, than having all the answers.
Quite simply, the crater poses this problem to the player. The sighting of the alien UFO's also plays on the mind in this very manner.

The idea of the "earth garden" can only be inferred by the notion of "what is not". There is absolutely no evidence of such a faculty in the game.
If anything the 5th garden may actually be the Ragnarok. Perhaps the crater was caused by the crash landing of a previous model.