After you visit three shrines on Great Sky Island, you gain the ability to reach Nachoyah Shrine.
Explore the Shrine
In the shrine, you will primarily use the Recall ability.
Go forward and use Recall on the raft, and jump onto it to be pulled to the other side. Jump off and press L to stop the Recall effect.
Farther ahead, a raft will fall into the water. Jump onto this raft and use Recall on it to go back up to the top of the waterfall. Notice that its path is marked by a line that is visible when you use Recall.
Turn left and use Recall on the cog wheel, and step on a cog to go up to the chest up above. Open it to get some arrows. Then you can use the cogwheel to go back down, or just jump into the water below.
There are some rotating clock hands up ahead. When these clock hands are both in the same position, the door opens, but since the clock hands are going in opposite directions, the door doesn't stay open long enough for you to go through. Use Recall on one of the hands when it is in the same position as the other hand, and while Recall is active, both of the hands will be in front of each other, keeping the door open. Go through, then deactivate Recall.
Check on the glowing object ahead to receive a fourth Light of Blessing.
From the shrine, you can go through the north door to find some Wings. You can optionally use one (place it in a rail and stand on it) to reach a floating island slightly to the west that is only accessible by Wing. On this island, you can jump down from the tall flat stone into the circle of plants to find a Korok.
From there, you can look southeast to see another floating island. If you want to go there, you should use the Purah Pad to travel back to Nachoyah Shrine and use a Wing from there. (Using a Wing Capsule on this island won't work because the Wing will just fall if it doesn't have a rail to gain speed.) When you reach the island that is northeast of Nachoyah Shrine, use Ultrahand to find a chest underwater, which contains a Large Zonai Charge.
If you haven't been to the floating island east of the Temple of Time, you can go to Gutanbac Shrine and use a Wing to get there. This island has a chest underwater as well.
You can try to land on top of the Temple of Time, but this is risky because there is no water to dive into there.
Go Back to the Temple of Time
Otherwise, you can use the Purah Pad to travel to the Ukouh Shrine, and from there go east to the Temple of Time.
At the Temple of Time
In the Temple of Time, use Recall on the wheels to reach the room up above, and pray to the Goddess Statue. You can ask for a Heart Container.
Afterward, try again to open the door behind the Goddess Statue. There will be a cutscene.
Now go toward the stone structure beyond the door. There is a gap in the bridge, but you can jump down onto the bridge segments below. At the end of the bridge, use Ascend to go to the upper level. At the next gap in the bridge, go down to the lower segment, go to the far end, and use Ascend at the end to go up to the next segment of the bridge.
Go to the platform at the end and check on the glowing object. There will be a cutscene.
Afterward, you will be on the northwest edge of the platform and can jump down from there to the kingdom of Hyrule. Hold R as you fall to position yourself above the water.