After the scene that you watch upon arriving from the Silent Realm, speak with the nearby Kikwi Elder. Afterwards, head towards the Great Tree and on the left path, towards the water.
Go into the water and begin to swim, but quickly descend to avoid the Quadro Baba. Continue to find an Amber Relic on the lakebed, then nearby should be a large hole. Swim through it.
Inside the Great Tree
You’ll begin in an underwater tunnel. You are to swim through it, and it isn’t all that long of a journey, especially considering how long Link can hold his breath. Nintendo went ahead and scattered a bunch of air bubbles (which fill up your breath supply) throughout here, so may as well get used to swimming. We’ll be doing quite a bit of it soon enough.
At the end of the tunnel, you’ll emerge into a large room. Climb the vinery nearby to a high ledge, then get onto the hanging platform. Take out your Gust Bellows and start blowing the Froaks into walls and stuff to get rid of them; try blowing one into the Bokoblin for convenience.
Make sure any other Froaks aren’t in your way, then line your facing up with the second platform and let those Bellows blow! Use it like a swing, where the wind is the force moving the swing, and dash and jump onto the platform when ready.
Defeat the Bokoblin and repeat the above process to reach the next hanging platform. There, exit the room to reach a ledge going around the Great Tree.
Outside, climb up to the ledge with the heart flower. Grab the aforementioned heart if needed, then look at the ledge on your right and down to find a Goddess Cube. You can jump down to it now if you really want, but you should save it for slightly later.
Instead, climb up the ledges towards the crown of the tree. Soon enough, you’ll come along to some vinery with Walltulas crawling all over it. Use the Slingshot and/or Gust Bellows to get rid of them, then climb up and left, jumping over the gap when it comes.
On the other side, look up to find some more Walltulas and a Deku Hornet nest. As annoying as it’ll be, you’ll need to shoot down the Walltulas and the Deku Hornet nest. For the latter, hope you have the Bug Net!
After getting stung half-a-dozen times, climb up the vines and continue the up-and-left thing. On the higher ledge, you’ll come across a room there. Go inside.
Here, you’ll find an oversized Moblin standing guard at the end of this very linear (and short) path. It would take you too long to beat him the old-fashioned way, trust me, so what to do?
I tend to dash straight at them with their shields up, kind of using the shield as a mini-ledge. Often, I manage to jump over successfully within a jump or two. Do whatever you want, then exit.
Back outside, utilize the nearby Bird Statue and simply go along the path set in front of you. Not much to mention along the way. You’ll have to fight a few Bokoblin, and an Amber Relic is in one of the nearby alcoves.
Speaking of those alcoves, go to the first one you come across and look over the edge of the ledge. On a below ledge, you’ll find a second Goddess Cube. Again, you can jump down to activate it now. But it’s probably a better idea to keep climbing the tree first.
From the alcove place, continue along the path to fight some Keese. Meh. A bit further along the path, you’ll find a ledge splitting off from the main path. Get on it and look down to find gasp another Goddess Cube. Like the others, try to ignore it for the time being.
Eventually Fi will tell you that you’ve reached the top of the tree. Nearby, you will find a Kikwi sleeping on a tree branch. Shoot ’im with the Slingshot to awaken him. Speak with for a while to learn of the gate in the south–and the trick to opening it.
Now you can go and activate those Goddess Cubes!
Goddess Cube 3
Starting from the top of the Great Tree, go back a bit to where there’s a ledge jutting out. It’s where some Keese were. While facing the Great Tree, carefully make Link hang below the path to the left of this ledge. If you look down, you should see Goddess Cube 3 to the left of a tightrope. Align yourself so you fall to the right of the tightrope, then go across it.
After activating the cube with your Skyward Strike, go to the nearest Bird Statue–probably the one at the top of the viewing platform, near the Deep Woods entrance. Choose to fly to the sky, then do a 180 and return to Faron Woods. Warp to the “The Great Tree” Bird Statue to look for the next cube.
Goddess Cube 2
From the Bird Statue, go forward to the nearby alcoves. Go to the edge of the path and “drop down” to make Link hang onto the path. Below, Goddess Cube 2 is sitting at the end of a grassy archway. Align yourself with the archway, then drop down and pull out your sailcloth.
As before, after activating the cube, return to the skies, then choose to descend to the “The Great Tree” Bird Statue again.
Goddess Cube 1
From the same Bird Statue, jump down to the ledges behind the Bird Statue. Head back to the ledge “stairway” near where you first emerged outside the Great Tree. If the Great Tree is on your left, keep your eyes peeled for Goddess Cube 1 below on the right.