After you give the Crystal Thread to Elle and receive Elle's Cape, you continue to the last tower, Tower 5.
Enter the Tower
When you enter the Tower, you are immobilized, and the Guardian shoots an orb of energy at you. If you are not wearing Elle's Cape, the orb will push you out of the tower. To get Elle's Cape, you have to give the Crystal Thread (obtained in Tower 4) to Elle in the Weaver's house, then sleep in the bed in the Elder's house twice. The next time you talk to Elle, she gives you Elle's Cape. Be sure to press SELECT to equip the cape.
When the orb hits Elle's Cape, the cape deflects the orb. Now you can go farther into the tower. Go up the stairs. Continue going up the stairs in each room until you reach a room with a bright door in the north wall. That door is a trap! Don't go inside! If you do, you will fall all the way down to the entrance of the tower and will need to go back up all of the stairs again.
Instead of going through the bright door, go east to the next screen. The Guardian appears and says that this is your final challenge. Go north through the dark door.
Go north and the lights will come on as you pass by. At the top, a monster comes out of a portal. This boss is called Shadowkeeper.
Shadowkeeper can shoot lasers from its mouth in three beams that spread out. You can block these beams with the X-Guard move, which you can perform by holding the R button. Shadowkeeper can also hit with its claws.
Your first task is to destroy the Shadowkeeper's claws. Hit them, but avoid Shadowkeeper's attacks. You can stand to the side, near the Shadowkeeper's face or near the bottom of the screen to avoid the laser beams while still inflicting damage. Run downward if Shadowkeeper pulls its claws back, because that means that it is about to hit with the claws. You can do a Slider attack straight upward at a claw, then instantly do another Slider downward to inflict damage twice and get out of the way without getting hurt.
When the claws are gone, Shadowkeeper starts attacking with the tail. The tail will glow green before it attacks, and it stops for a moment before attacking, so be ready to run downward when the tail glows green and stops. Meanwhile, hit the Shadowkeeper's face to inflict damage, standing to the left or right to avoid the laser beams. Eventually, its face will be damaged and it won't be able to spit laser beams anymore. Just keep hitting its face until it dies.
After Shadowkeeper is gone, the Guardian tells you to go back and talk to the Elder. Australia is resurrected and everyone else in town is revived.
Secret Polynese Resurrection
Go south from Tower 4, past the mountains, and step on the area that looks like it has ruins on it. You'll be in a small dungeon. Go north, killing any Whisps and Living Statues that get in your way, then enter the gate at the top. You will resurrect Polynese.
Secret Mu Resurrection
There is a secret area that you can find if you go as far north from Tower 3 as you can go. There is a small peninsula north of some mountains, and if you walk on the correct spot, you will enter an unmarked area on the map.
This area has several boulders blocking your path. Go to the rightmost boulder and push it up, then go up the middle path. Push the boulder up only enough to walk to the right. Go right and push the boulder up, then go left and push the boulder left. From there, go north and go through the gate. You will resurrect Mu.
Visit the Hole
Go back to your town and talk to the Elder. He asks you to come outside and go east, where there is a huge hole. Leave the village, then go east to a narrow piece of land with something in the center. Walk on that spot to find the hole. Go to the top of the hole to find the Elder. Talk to him. He will say that although you have revived the land on the surface, the plants and animals still need to be revived. You must fall into the hole to reach the surface world, but once you go, you can't come back until your task is done. If you wish, you can go back and check on Elle, or buy supplies.
When you are ready, go back to the hole and tell the Elder that you are ready to go. He reminds you that your CrystaSpear can only heal you when you are in the underworld, so you should use Bulbs to heal up on the surface world. When you are ready, stand to the left of the Elder and walk downward to fall into the hole. After a cut scene, you begin Chapter 2: Resurrection of the World, where your first destination is Evergreen and the Ra Tree.