Upon leaving the Moonlit Grotto you'll see cutscene with Queen Ambi and Naryu-- the Black Tower is almost completed. The Maku Tree will tell you of an essence to the Northwest of Lynna, our next destination. Head up and you'll see two Tokay prodding Dimitri, who has washed ashore. Talk to them and they'll trade you two Ember Seeds for Dimitri. Hop on Dimitri and head out into the sea.

Head back to the shore (to the left, about two screens). Head over to Lynna City. This is where the game splits. There are three possible paths from here.

Buy a flute from the Shop for 150 Rupees- You will get Dimitri
Do nothing- You'll get Moosh
Get the flute from the Shooting Game (Past)- You'll get Ricky

If you're playing a linked game then go here.

Now, search the Nuun Highlands for the three workers. Depending on who you choose the search will inceasingly difficult. Moosh's apth is the hardest. I would choose Dimitri or Ricky. In any case, when you find all three, you'll automatically go back to the Boss carpenter. The workers will finish the bridge and you can cross, huzzah!

Go across the bridge, up past the Dark Nuts and up into Symmetry City. Apparently a Volcano erupted, so there's not much to see. Go left and get the Gale Seeds from the tree. Chop the rightmost and left most bushes to find Time Warps. Play the Song of Echoes and transport back in time.

Go into the big hosue and talk to the girl on the left. She'll tell you about the Tuni Nut. Head to the op-right house in town to get the Tuni Nut from the guy there. Now, go down, left twice, down, left, up, and dive into the top-right-most square of water. Swim through the tunnel and you'll meet Tokkey, the music researcher. Play the Song of Echoes for him and he'll teach you the Song of Currents.

IN DEPTH - The Song of Currents
You can use the song to transport from the past to the present. Not the other way around. Think of the Mirror in LttP allowing you to go from Dark > Light not Light > Dark. Oddly, it leaves a warp point (visible on the map too) just like the Mirror did.

Go back in time. Go down and push the vine to the other cliff. Now, go up to the cliff and go inside the cave. Take the stairs on the bottom right and push the red rock to the left. Now, go abck down to the vine and use the Song of Currents to go to the Present. Climb up the vines to the new pool of water.

IN DEPTH- Water Shift
If you leave the vine on the left cliff and climb up in the present- when the water is drained, there'll be a small pool with a sign saying to not throw anything in. Instead throw a bomb in. A fairy will appear asking if you threw in a Gold Bomb, Silver Bomb, or a regular bomb. Be smart and choose regular bomb and the fairy will give you an ugrade to your bombs allowing you to hold 30.

Climb up the wall dodging the boulders. WHen your each the second screen, go only up the middle path. The other two are dead ends. Once at the top, go into the cave to reach Patch. Talk to him about the Tuni Nut and he'll have you follow him downstairs to another damn minigame.

Alright, this is hard. What will happen is you're in a sqaure room with a track running on the perimeter of the room. If the cart hits the Tuni Nut before you can knock all four beetles that appear into a hole, that's the end. But, if you stand on the switch, the track will change so that the cart can pass safely by the Nut, buying you precious time. Use the sword to know the four beetles into the pit. Try to stay on the switch when the cart gets close and don't fall off. When its all over you get the Tuni Nut, all nice a fixed.

Leave the cave, go right, jump down, and head up into Symmetry Village. Place the nut on the pedestal in the big hosue and the town will be saved. Now, go abck to the present and the way to the fourth dungeon will be open.