After you visit three shrines, you can return to the Temple of Time and open the door.
Open the Closed Door
After you have completed three shrines, go back to the Temple of Time. Check on the glowing symbol on the door, then go inside. Go up the stairs and examine the glowing object. After the cutscene, you will have the Recall ability.
Go to one side of the room, next to one of the spinning waterwheels. Use Recall on it and you can stand on it to reach the platform between the two wheels. Press the indicated button when you reach the platform, to stop the Recall effect. Then use Recall on the center wheel next to the platform that you are on, and stand on it to reach the area up above.
There is a Goddess Statue here, but nothing special happens when you pray to it. Go to the door behind the statue and examine it, then hold the indicated button to try to open it, but you will automatically stop before your health runs out. There will be a cutscene, during which the Purah Pad will become able to teleport you to shrines and other locations that are glowing blue on the map.
The location of the next shrine is marked on your map. Use the Purah Pad now to travel to the Room of Awakening, at the southernmost end of the Great Sky Island.
Reach the Upper Area
From where you arrive, walk under the stone platform that is near the rotating wheel, and use Ascend to go onto the top. Then use Recall on the spinning wheel to reverse it, and when you reach the other side, do the same with the next wheel. This will allow you to reach a tunnel up above.
Go to the end of the tunnel and you will find a shrine at the end.
Note also that there is a Construct in this room that can make Energy Wells, but you need a large number of Crystallized Charges to make one, so just keep this location in mind for later.
Check on the glowing object to open the shrine, and go into the Nachoyah Shrine.