Successfully complete the game on the hard difficulty setting. The Up & Down level will shimmer, and you can now access both 2D bonus levels:
Passage From Genesis level
As you start the Up & Down level, swim around the cavern until you find the Info Crystal. Below it is a hole that leads downward. The current is too strong -- you cannot swim down it. Look for the boulder just right outside the alcove where the hole is located. Push it into the hole and stay directly behind it. You will enter a room with four stone pegs. Above those pegs is the power of Sonar. Get the Sonar and use it in the small opening of the pegs. A little light should appear. Quickly light up all four and a door below will open to the 2D level.
Pathways From Nowhere level
After you make your way up the geyser, you will find a big ring with a spot of light in the middle. In that same area are many power jewels. Find them and bring them to the ring. Two are above the water, one is under the stone shack-like thing, and the rest are around the other side of the pool. After you have collected all of them. it will open the way to the bonus area.