After you solve the mystery of the mural at Dracozu Lake, the Thunderhead Isles become accessible.
Reach the Thunderhead Isles
After you have made progress in the Secret of the Ring Ruins quest, you can use the Popla Foothills Skyview Tower to reach the Thunderhead Isles.
Prepare to Cross the Thunderhead Isles
Make your way southeast along the islands. Keep in mind that since it is raining, you will slip down the walls unless you have special armor or use elixirs to prevent it. Most of these islands have islands beneath them, so you can use Ascend to go to the top. There are some Soldier Constructs along the way.
Use the Launcher
Eventually, you find a dragon statue with a lightbulb in front of it. There is an angled stone, and the dragon statue's wire is connected to that stone. Stand in front of the angled stone, and after a while, lightning will hit the dragon statue's horn, powering the angled stone, which will launch you to the next island.
Get an Old Map
Attach two wooden boards together and place them on the gap in the stairs, but beware of the Electric Wizzrobe that is patrolling the area at the top of the stairs.
West of this area, there is an island where you will find a treasure chest that contains a Topaz.
Go east from there, then continue to go southeast. There is a platform to the west with a dragon statue that has a lightbulb in front of it. Shoot a Bomb Flower at the boulders above this statue, then stand on the bars in front of it. Eventually, lightning will hit the statue's horns, removing the bars from beneath you, allowing you to reach the treasure chest below. It contains an Old Map.
Use the Makeshift Rail Cart
Use Ascend to get out of the room with the treasure chest. You can use Ascend again if you want to fight the two Constructs on the roof.
Then go east and you reach a rail station. You can optionally use Ascend to fight the Constructs on the roof. Otherwise, at the rail station, you will see a metallic plate on the rail. The metallic plate has another metallic plate attached to it in a T-shape, allowing it to stay on the rail. Lift it up out of the broken rail, then place it on the non-broken rail. To stay safe from the lightning that will strike the metal plate, attach a wooden board flat on top of it that you can stand on. Then attach a fan to the back of it, jump on, and hit the fan.
At the other end of the rail, hit the fan to stop it from using power. Use Ascend to reach the upper area, then notice the treasure chest on the column in the water. There is a cube floating in the water, and two wooden crates under the roof nearby, so attach the crates to the cube and climb up so you can reach the chest.
Reach the Shrine
Glide southwest to the island down below where you can see several Constructs. Defeat the Constructs, then take the long wooden board and attach the smaller boards in a T-shape, like the metal cart that you rode on earlier. Flip it over and place it on the rail with the T-shaped part in the middle. Then get a Fan and attach it to the back, get on the wooden board, and hit the fan, but before you reach the end, use Ascend to enter the area floating above the rail. This allows you to reach Joku-Usin Shrine.
Reach a Chest
There are some stairs in the north corner of this room. Go to the top of these stairs, then use Ascend on the pillar that hangs down above these stairs. You will exit the enclosed area.
There is an optional area to the northeast where you can try to get the treasure chest that is guarded by a Flux Construct III.
Otherwise, you can go east and try the Device Dispenser if you wish.
Then go east down the stairs to find a room guarded by Like Likes. You can drop (not throw) bomb flowers, and use Ultrahand to place the bomb flowers in front of the Like Likes, to make them eat the bombs, then shoot their cores with arrows. Or, if you are patient, you can try to attach the metal cubes together and place the line of cubes partly outside so lightning will hit it and shock the Like Likes. The chest that they are guarding contains a Big Battery.
Use a Rocket Cart
Then use Ascend to go to the roof of the Like Like building, and rotate the wheel (it will get stuck if you turn it the wrong way) until it stops and the angled block is pointing southeast. Stand in front of the angled block and wait for lightning to power it, launching you to the next island.
Go southwest and attach a small stone slab to the large stone slab in a T-shape, flip it over, and place it on the rail, then attach a rocket to the back. Stand on the stone slab and hit the rocket. Then open the chest in the building at the top.
Reach the Far Cart
Glide northeast to where you were, and take the wooden boards attached in a T-shape, and place one in the distant unbroken rail. Then make another T-shaped board and place it in the nearer rail. Then attach wooden boards and logs to the end of the near one to create a bridge to the far one, but don't attach anything to the far one. Then when you can safely reach the far cart, get a fan and attach it to the distant cart. Stand on the distant cart and hit the fan to reach the next area.
Reach the Next Isle
Go down the stairs, then go clockwise around the area, defeating the Constructs. Then when you can't go farther, drop down to the area below, and follow the curving path southeast. Use Ascend at the end to reach the next island. Defeat the construct here, then find the pillar that is hanging down, and use Ascend on it. You can go northwest and walk slowly across the metal to reach a chest that contains a Mighty Zonaite Shield. Then go southeast and use Ascend on the pillar that hangs down.
Glide east to where you see a dragon statue with a lightbulb. Stand in front of the angled stone and wait for lightning. When you land, open the treasure chest to get 3 Shock Emitters. Then follow the path and you reach a ledge with a glowing circle on the end. Stand on the circle and press the button to jump. You will reach Dragonhead Isle.
Glide down through the dragon's eye to reach the shrine. Open its door. This shrine doesn't have a puzzle, so go in to get a Diamond and a Light of Blessing.
Exit the shrine and cut or burn the vines to the north. Beyond where the vines were, you can optionally go west to find a Goddess Statue to pray to.
Required Number of Hearts
Otherwise, go to the door in the north wall. You will need at least 10 Heart Containers to open it, and you will get a Game Over if you don't let go before you die, so be sure to let go if you don't have enough.
Once you open it, go forward and examine the glowing object. This completes the quest, and begins Guidance from Ages Past.