After finding GreenWood empty, you go east to the LostSide Marsh and find the Water Shrine.
Water Shrine 1F
From the entrance of the Water Shrine, go left. There is a Mudpit lair nearby. There is also a Shaber dragon that will jump out of the water. Kill the Mudpits to create a bridge to the middle of the temple.
Use the new bridge to reach a Shrubber lair to the north. Defeat them to free a squirrel. You will hear the squirrel saying that it is hungry and that if someone comes to feed it, the squirrel will give that person a powerful sword.
After releasing the squirrel, go to the southwest corner of the Water Shrine and go down the stairs.
Water Shrine B1F
To the north, there is a Mudpit lair as well as some Shaber dragons guarding it. Defeating the Mudpits will create a bridge to the next area.
Go east. While avoiding more Shaber dragons, defeat the Shrubbers that you encounter. After you do, you will release a bird.
Go east, then south. There is water to the right. When you go past the water, go to the east side of the water and then go north to find a Shrubber lair. Defeat the Shrubbers to remove the waterfalls and gain access to a chest that contains 150 GEMs.
Go back the way that you came, then go west. There are some Floor Spears coming up out of the ground. You can't damage them with your current sword, but you can temporarily paralyze them. The spears rotate around, so they are easy to avoid. Kill the Mudpits to make a blue crystal appear. Talk to the Crystal Fairy to receive EXP. She can send you back to GreenWood if you wish. Otherwise, continue on.
There is a chest containing a Medical Herb nearby. Kill the Mudpits to release a mole. The mole will say that it can bring light to the darkness. Go down the stairs.
Water Shrine B2F
After going west, go south. Clear the the Shrubber lair to reveal a new passage with a chest that contains delicious seeds.
The next area of the Water Shrine is dark, so you need to go back to GreenWood and talk to the mole that you released. Go upstairs and talk to the Crystal Fairy to be returned to GreenWood.
Get a New Sword
Go to the house of the squirrel that said it was hungry. Equip the delicious seeds to get the Psycho Sword. Equip it if you are level 5 or higher. If you aren't, you won't be able to swing it. The Psycho Sword has the ability to temporarly paralyze invincible monsters, such as the metallic monsters that you couldn't defeat in the World of Evil painting. You can't kill them with this sword, but you can paralyze them.
Meet the Soul of Light
Next, go visit that mole that said it can bring light to the darkness. The mole is actually a heavenly being like you. It will join you. After that, if you are in a dark area, the soul that spins around you will shine light. It can also reveal certain invisible monsters.
Water Shrine B2F, part 2
Now return to the Water Shrine, to the basement where you got the delicious seeds. To the north of the stairway is a Mudpit lair. Clearing it reveals a side room with a Shrubber lair. Defeat the Shrubbers to release a crocodile.
To the north is a Mudpit lair. It opens a side room. Step on the center tile to get a Strange Bottle. If you equip this item, it will prevent you from losing any GEMs if you die.
Continue going north. Make the Soul of Light shine on the statues. One of the statues will still look dark even when the Soul of Light shines on it. The dark statue is a Demon Statue. When you approach it, it will teleport to a random location and shoot an energy ball out of its mouth. Kill it to clear the lair and release a squirrel.
Go east to reach an area where two of the statues are Demon Statues. Kill them to clear the lair and release a mole.
Go south until you find a Mudpit lair in a side room. Clear the lair to reveal a chest in the small room to the east. It contains 50 GEMs.
Go north from the Mudpit room. Go up the stairs and kill the Demon Statue. You will release a deer.
Go east, and go up the stairs there. Then go west and kill the Mudpits. Clear the lair to create a bridge to the lower part of the Water Shrine. This creates a quick shortcut to the entrance.
Go west from where you fought the Mudpits to find a chest. Be careful: a Shaber dragon jumps out of the water directly in front of the chest, so be sure to kill it before you open the chest. The chest contains 50 GEMs.
Go north to exit the Water Shrine. Just north of the Water Shrine, there is a Mudpit lair. Clear it to release a dog.
Go east from there, to an island where a couple of Shaber dragons pop out of the water. Go south from there to find a Shrubber lair. Kill the Shrubbers to reveal a warp tile to the GreenWood shrine.
Go north from the warp tile that you just created, then go west until you reach an island with a Lotus Plant on it. The Lotus Plant is not associated with a monster lair. It spits out butterflies. To the east, a Shaber dragon jumps out of the water just west of a stone pillar. East of there, there is a Shrubber lair. Kill the Shrubbers and clear the lair to create a bridge to the Fire Shrine.