This page explains how to find the Ya Naga shrine and solve the "Shatter the Heavens" puzzle.
How to Reach the Shrine
Go to the top of Lake Tower and float north to the islands that are west of the Bridge of Hylia. There is a shrine in the middle of the largest of these islands.
How to Solve the Shrine
Go up to the top of the stairs and put a square bomb on top of the stone cube. Then go down to the launcher below the stone cube and put a round bomb into it. Detonate the round bomb to make the stone cube go to the ceiling. Quickly switch to your square bomb rune and detonate the square bomb when the stone cube reaches the ceiling. If done correctly, the cracked blocks in the ceiling will shatter.
Next, put a round bomb into the launcher, then stand on top of the stone cube. Detonate the bomb and you will be launched upward.
Use the paraglider before you start falling downward, then float to the treasure chest on a pillar nearby. It contains an Eightfold Blade.
Then go talk to Ya Naga to get the Spirit Orb.