Once you have entered the cavern, keep an eye out for these buldging grey pods. They act just like treasure chests, and can have an item in them for you. There are a lot of MBulbs scattered through out this cave plus other goodies too.
The cavern is only a few floors deep; the first floor and three levels of basement. As soon as Ark stands up in the tree, he is in a small room. There is another save point if you want to use it and also a doorway. Just go through the doorway and you'll end up in a long corridor and on the first floor. Follow the corridor until you reach a three-way fork in the road; there are paths left, right and a staircase down in front of you.
If you decide to go right, you'll meet up with one of the monsters in the cavern. This big monkey guy will curl himself up in a ball and hurl himself at you. Often times they'll just jump down from the ceiling in front of you in pairs and attack. Luckly there is only one in the way. There is a door that goes into another room toward the bottom half of the screen. If you go through the door, you'll come across a big hole, but you'll be on the north side of the hole, and there is also a south side of the hole (which is the path to the left from the three-way split in the pathway). You can fall down this hole from here if you would like, but you'll just end up on the wrong side of Basement1, so you may want to go left from the three-way fork.
Continuing left from the three-way split, you just follow the path that the cavern takes. There's really no way to get lost on this level. Ark will eventually destroy a yellow flower monster that turns into a spirit. The spirit explains that all the plants came from the same tree. If Ark saves the tree, the world will become green again. The spirit is even nice enough to fill up some of your HP too.
To the right of the spirit appears to be a dead end. There looks like there is a path on the other side of the water, but there's no way of getting to it. What needs to be done in order to create the bridge is to destroy the two fish that are swiming and jumping. Once those two are gone the bridge will be created and you can continue on. Now you are on the south end of the large hole that you saw earlier. Go ahead and jump down the hole.
In Basement2 head west. Then follow the cavern north and go down the stairs.
Ark will now be on Basement3. Head to the west and pick up the three treasures, then head south. Follow the cave and then head south when you get to a north/south split in the path. Continue following the cave until you get to a rock barrier. Ark will have to push the rock out of the way in order to move on. Walk northward until you destroy a monster that turns into a spirit. The spirit will request that Ark follow it. Jump over the gaps that are in the floor to follow the spirit and then climb down the long vine.
At the bottom there is a large pool of water with some very beautiful plants. Talk to the purple lily and it will thank Ark for saving it. The lily will also give Ark the Giant Leaves, which will allow you to swim through water. Swim to the lower left corner of the pool and pick up a MagiRock. Another flower will mention a "Parasite" who lives in an area filled with poisonous gas. Climb back up the vine to get back to Basement3.
Go past the rock you have to push and head tword the staircase in the northeast section of the room (the northern path at that previous north/south fork). Climb down the staircase and now you can swim across the pool of water that was preventing you from getting to the other side. The next few levels just have staircases in them. When you get down to the bottom floor, there will be another lily there. Talk to it and it will give you the Ra Dewdrop, which is an antidote to the Parasite's poisonous gas. If you would like, continue swimming east and talk to the other flowers and pick up the treasure. Leave the bottom floor and head back to Basement2.
Now that you're back on the floor that you ended up at when you jumped through the hole, swim across the creek to get to the other side. If you haven't already, get the RaSpear and other treasures. The doorway to the Parasite is in the northeast corner. Before entering the door, equip the Ra Dewdrop and then use it. Ark will then become immune to the Parasite's poison.
Once you defeat Parasite, you'll return back outside the cave. Hey, everything is green again! Talk to the tree that you had crawled under and it will explain that it is the Ra Tree. The world is now covered in green plants again, but it is still too early for the world to be fully resurrected. Some of the plants in the area mention that there use to be a paradise of birds up north. Leave the Ra Tree and travel north.