Instructions
Play through the "Test of True Courage" section of the game, which is located in Area 44. This mission is located near the end of the game.
Proceed through the level by avoiding monsters, as they are difficult to kill. Completely avoid them instead.
Press start to access your "Equipment" screen. Select your whip to equip it as your weapon. Press "B" to use it to get across ravine areas that you otherwise could not access. Destroy rocks in your path by equipping your pickaxe in the same method and pressing "B" to use it.
Fight against the doppelgangers at the end of the stage, then read the story text completely. Joch will tell you that they are going to raise the sunken island to revive the Mana Fortress. You are warped out of the level immediately.
Talk to Flammie to get him to fly you to the Sunken Isle. Fly southeast as far as you can to find the Tree Fortress. Talk to the Emperor there to advance the story. Finishing this section of the game will cause the Sunken Isle to rise.
Fly to the northeastern most point of the game map to find the Sunken Isle. Enter it to begin the final portions of the game.