Okay...you want someone to explain trees? Here\'s my idea:
Caves are created by the flow of water, eroding the rock, correct? Because the acidity of the water flowing past the stone dissolves the minerals in the stone, which are swept away (or, more accurately, dripped away) to later land on something, wherin the water evaporates and leaves the minerals to form a small deposit, which eventually grows to form a stalagmite, unless, of course, the water is not given a chance to evaporate and is swept off someplace eles (i.e. an underground river). Well, to make a cave as big as the one Ylaikum exists in, you have to have a whole hell of a lot of water, and a whole hell of a lot of drainage. The water is provided by the natural cycle of evaporation-condensation-precipitation ocurring on the surface (we can assume that a decent-sized river or stream once flowed into the ground, perhaps by means of a rift caused by an earthquake). My theory is that the water drained into the lake, then out the bottom of the lake through another rift, perhaps caused again by the movement of our friends the tectonic plates. This water could have also trickled down the walls and helped to form the Labyrinth (which also could\'ve been formed by similar conditions as the ones explained above, but on a much smaller scale). Now, as you should know, the water in rivers and streams carry a great deal of sediments and nutrients along with them, not to mention the minerals (such as nitrogen, which is essential in the growth of plant life) that were dissolved from the stone. As, over time, the strength and amount of water pouring from the ceiling of the cave decreased, it deposits all the sediments. minerals, and nutrients onto the ledges of stone and according levels of the great cave it has created. This formed the basis of nutrient-rich, life-supporting soil that exists in Yliakum and the surrounding levels. The Azure Sun (the large, radioactive blue crystal) merely helps to replenish these nutrients and keep the people, plants, and other life going.
But that\'s only if you want to get all technical.
Satisfied?
Oh, and by the way, if you need this kind of explaination for every aspect of the game, I suggest you leave so that those of us with imagination can enjoy ourselves.