After you speak to the old woman in the Sealed Grounds, you reach Faron Woods.
Catch the Kikwi
Be sure to use the Bird Statue here to add it to your list of surface destinations.
Just past the entrance to Faron Woods, there is a rope hanging over a gap. Dash to it, and you will automatically grab it. Then follow the on-screen instructions to swing. Press the indicated button to jump off of the rope to the other side.
One of the small trees up ahead has a glowing spot on it. If you cut this spot, you can get rupees. You can cut the tree once to make it fall, then keep cutting at the falling tree until you cut the glowing spot.
There are some trees blocking the path. Use a downward chop to split them down the middle and get rid of them.
Just past that, there are a couple of red Bokoblins harassing a forest creature. Defeat the Bokoblins and check on the creature, and it will run away. In the Wii and Wii U versions, Fi will tell you about the creature.
Run up the hill that the Kikwi ran up, and you will soon find the Kikwi, which will run away again. You will find a Bird Statue nearby, so check on it to add it to your list of Surface destinations.
To find the Kikwi, use Dowsing to search for Zelda, and it will point to the Kikwi. It is hiding behind the mushrooms nearby. Hit the mushroom with your sword to get the Kikwi to pop out again.
If you see a glittering mushroom, you can hit it with your sword, then use an empty bottle to catch the Glittering Spores. You can use them to transform Green Rupees into a random color rupee (including black Rupoors, which reduce your rupees); you can use them on recovery hearts to turn them into fairies; you can use them to stun enemies; and you can use them on insects to slow them down (this is more useful after you get the Bug Net, which you can't get yet). Your bottle will hold five doses of Glittering Spores.
As you continue along, you will encounter some Deku Babas. Remember to slash in the appropriate direction according to how their mouths are shaped.
Eventually the Kikwi will hide behind a tree. Just talk to it this time. Machi will tell you that Zelda escaped with the Kikwi elder.
Find the Elder
Fi suggests using dowsing to find the elder. When you dowse, you will see that you should go back the way you came. However, before you do, walk over to the log near Machi and push it off of the ledge. This will give you a shortcut, and it will also reveal an Amber Relic. If you find another Amber Relic, you can return to the Skyloft Bazaar and have Gondo upgrade your Wooden Shield.
Now go toward the dowsing signal. It leads to the east. Dash up the ramp, ignoring the Deku Baba as you run past, then pick up a rock from the top of the hill and throw or roll it at the Deku Baba to kill it. Press the Help button while holding a boulder to find out how to throw and roll things.
You will encounter some Red Bokoblins up ahead, and a Grass Octorok. To defeat the Octorok from a distance, do a Shield Bash when the rock is about to hit. The rock will bounce off and hit the Octorok, killing it. If you raise your shield but you don't time your Shield Bash correctly when the rock hits you, your shield will be damaged. If you don't have a shield, you can swing your sword to knock the rock back at the Octorok.
Be sure to push the log off the ledge here to create another shortcut, near the Bird Statue from earlier. This log also has an Amber Relic, so feel free to go back to Skyloft and visit Gondo at the Bazaar to have him upgrade your Wooden Shield. If you don't have any Monster Claws or Jelly Blobs, sleep in a bed until night time, then go outside and kill Keese and Chuchus until you have at least one of each. Then you can pay Gondo 30 rupees to upgrade your Wooden Shield to a Banded Shield. Be sure to equip the Banded Shield afterward. Then choose the "In The Woods" Bird Statue to return to this area, and climb up the log to reach the ledge nearby.
Go up the hill and do a downward chop to get rid of more trees in the way. Continue along the path, and soon you will reach a rope that is tied to a tuft of grass. Cut it, then swing across the gap with it.
Go forward and talk to the big blob-like creature. This is Bucha, the Kikwi elder. He's too worried about the other missing Kikwis to talk about Zelda.
Find the Missing Kikwis
Fi will add the Kikwis as a dowsing option. Switch your Dowsing setting to the Kikwis.
Look around the platform to find a tree with a hollow spot at the bottom. Walk toward the hollow spot to automatically climb in. Climb up the vines beyond. There is a rope ahead that you must walk along. Follow the on-screen directions to avoid falling off. You can jiggle left and right as needed to stay balanced. When you are getting close to a burr, stop moving forward. If the burr latches onto you, it will eventually explode. Follow the on-screen instructions to jostle. If done correctly, you will shake the rope and make the nearest burr fall off, but if you are too far off balance when you do this, you will fall. If you fall but are still holding the rope, you can move upward to climb back up.
Soon you reach a clearing where a Red Bokoblin will summon a gang of other Bokoblins. Get rid of them, then the Kikwi will ask for help getting down from the tree. Fi will also give you some advice (optional in the Nintendo Switch version). To get it down, do a roll attack into the tree. The Kikwi will fall off the tree and introduce itself.
Approach the rope and press the indicated button to grab it, then use it to swing to the nearby ledge. Push the log down, then hop down.
A Guay is nearby. They actually attack by pooping on your head. If this happens, it drains your stamina. Do a spin attack to get that stuff off of your head.
You will see a stone structure up ahead. There is a Red Bokoblin guarding it. Go up the stairs and you will find a symbol on the ground, as well as a cave entrance on a ledge that you can't reach. Go to the top of the stone structure to find a Bird Statue. Fi will recommend using this vantage point to dowse for Kikwis. One seems to be behind an area with a grey stone almost straight ahead, and the other seems to be on a ledge near a big brown rock.
Go down the stairs and go to the right. There will be Guays and Bokoblins on the way. Up ahead, you will see three Bokoblins around a tree. There is a narrow ramp northeast of this tree. Go up this ramp. At the end, you will see some vines. Dash up the wall to reach them, then go to the left, and follow the on-screen instructions to leap to the next section of vines to the left. Be sure to grab the stamina fruit along the way. Then drop down when you reach the ledge.
There is a Kikwi hiding in the grass here. Cut the grass and the Kikwi will crawl around trying to hide. Keep cutting the grass until you get the option to talk to the Kikwi, named Erla.
Drop down from the ledge and find a gap in the tree root to the south. Crawl through, then kill the Octorok nearby.
Then go to the right, where you can drop down a couple of ledges and push a log off of a tall ledge. This gives you yet another shortcut.
Go back up the two short ledges. Look for an Octorok nearby that is in front of a narrow slope. Go up that slope and go to the left to find a rope leading to a Piece of Heart.
Go back across the rope, and go along the narrow strip of grass, kill the Deku Baba, and continue along the path to find an area with a short brick wall around the far edge. Kill the Octorok in this area, then go past the grass to find a hole in the ground next to the tree. Fall down that hole, then go through the nearby tunnel to find a Kikwi hiding next to a regular tuft of grass. Try picking up the Kikwi and it will speak. It is called Oolo.
Get the Slingshot
Now go back and talk to the Elder. You can drop down from the gap in the brick wall in this area, then go southeast toward the Elder. Check your map if you can't find him. You can use the map to place a beacon on him if needed. When you talk to him, he tells you that Zelda went to the temple in the woods, which is past the stone structure that you found earlier.
The Elder will give you the Slingshot. Just dash up the Elder's back to get it, then hop back down afterward.
If you run out of Slingshot seeds, you can get more from yellow fruits, and from curly green plants.
Use the Slingshot to shoot the nearby curled-up vine.
Now is a good time to return to Skyloft, because you can now use the Slingshot to get access to Beedle's Airshop. If you are playing the Nintendo Switch version and have the Zelda and Loftwing amiibo, you can use it to go back to the sky now. Otherwise, swing across on the vine that you shot down, and go forward until you see a small pond to the right. Swim across the small pond to return to the Bird Statue on the Viewing Platform. Use it to return to the sky.
Shop at Beedle's
Fly back to Skyloft, then follow Beedle's Airshop, which is the flying building with the large bell under it. When it gets close, use the Slingshot to ring the bell. Beedle will lower a rope. Walk up to the rope and grab it. You may need to walk around a bit before you get the option to grab the rope. Then the rope will lift you up onto the shop. When the rope is above the wooden walkway, let go of the rope and go inside.
Buy a Bug Net. It's 50 rupees, which you probably have by now. You can also get an Extra Wallet for 100 rupees, so save up for that if you don't have enough yet. To leave the airshop, go outside and fall off, then use the Sailcloth to land safely.
Now you can go around Skyloft and practice catching bugs. You can swing the net the same way that you swing the sword. Try slowly sweeping the net toward the bugs. Quick slashes will only result in small movements of the net. There are Blessed Butterflies south of the Knight Academy, a Sky Stag Beetle on the southern wall of the Knight Academy, Skyloft Mantises around the side of the Goddess Statue area, and Starry Fireflies around the river at night. If you have potions, you can talk to Bertie at the Potion Shop in the Skyloft Bazaar to upgrade your potions with the bugs that you have.
When you're ready, fly back to the Green Column and return to Faron Woods, to the Viewing Platform location. There is a ledge in the back. Just shoot the Slingshot at the rolled up vine above the entrance. In the Wii and Wii U Versions, Fi will have some advice (optional in the Nintendo Switch version). Climb up the vine and swing to the ledge. Walk into the entrance, and there will be a brief cutscene. Then you will reach the Deep Woods.