After Sub-C is shipwrecked in a storm, you drink some coconut milk and venture into the first cave.
Explore the Cave
Go north from the entrance.
Kill the Dodos to open the north door. Go through.
Jump on the northeast tile to reveal a switch. Jump onto it, then jump west and get the Bolas. This is a weapon that you can throw. To use it, you can either press SELECT to select it, or you can press START to pause the game, then use the directional pad to select it.
After you get the Bolas, kill the Dodos to open the north door, and go through.
There are four Ninja-monkeys hopping around in this room. You might find it helpful to throw Bolas at them when they jump far away. When you have killed them all, go north through the door.
There are even more Ninja-monkeys here. Kill them all, then go north through the door.
You can throw Bolas to the north to kill the Looper snake there. Then jump onto the tile on the left, then step on the switch on the right. If you ran out of Bolas and couldn't defeat the Looper to the north, kill it with the Star/Yo-yo now, and carefully get the Bola from the middle of the room, but jump immediately to avoid the two Loopers that charge toward you. Kill the Loopers to open the north door. Go through.
Don't jump onto the tiles right away. The middle tiles disappear and reappear. Wait for the southernmost tile to reappear, then quickly jump north, but jump onto the west tile before you go all the way north. This makes a double heart appear. You can also jump onto the east tile to make another double heart appear. Take the hearts, then when you're ready, carefully jump north to go to the next room.
Be careful of the Bonehead birds here. They can jump over the water. Kill all the Boneheads and Dodos to open the west door. Go through.
Right after you enter this room, it goes dark. Carefully jump onto the tile to the north. If you don't remember where it is, walk east until you are up against the door that you just came through, then go west twice, then jump north. This tile will light up the room. Jump onto the tile to the north to make a switch appear. Step on the switch to open the north door. (The west exit goes to a room with a wrong exit: stairs that take you back to the entrance of this dungeon. So just ignore it.) Go through the north door, then keep going north to reach the second overworld area of chapter 3.