Get back to Skyloft, then head back to the Goddess Statue. Inside, put the Amber Tablet in its location. Fi will then appear and inform you that a third beam of light appeared to the southwest of the island. Leave the statue and fly towards this new yellow beam of light...
Upon you arrival, Fi introduces you to the Lanayru Mine, an arid land that quickly turned into a desert. Go down the ladder, go behind the huge tower and perform a Skyward Strike at the Goddess Cube. Try speaking to the two half-buried robots, then head to the Bird Statue and take a look at it. Go north, then upon reaching the end of the path, push the cart until it falls down. Jump down, pull it a few meters, then push it against the next wall. Afterwards, climb on it, climb higher and go on. Go left to reach a huge round area with a strange stone in the centre, other little robots and lots of machineries.
Hit the stone with your sword and the whole area will come back to life! Talk to the little robot next to the stone that says that they are extracting Timeshift Stones to bring them to the Lanayru Mining Facility. Fi has detected a "time shift" and says that the impact on the blue stone rewound the time. This place is now the way it was in the past. Talk to the busy little robots and pick up the Ancient Flower southeast. Then, get into the cart to the south which will bring you to a cave north. Talk to the two robots, then pick up 20 rupees in the chest. Get back into the cart to get out, then come back to the tunnel where you came from and cross the time barrier. Refill your bombs and push the cart to the next barrier to get into the next "room".
Blow up the rock next to the barrier, then hit the Timeshift Stone (blue crystal) to bring back this place to life. Take a look at the statue and notice some sort of bowl in front of it. Throw a bomb into this bowl, which will make the statue fall down. Go ahead, then rush to go through the quicksands towards the Stamina fruit. Throw another bomb into the closest statue's bowl, then head to this statue and do the same on the three other statues to pick up rupees and find bugs inside the pots. Then run to the next Stamina fruit and go on up to the next room, where there are some Electro Spumes.
To get rid of them, shoot a Deku nut to stun them, then throw a bomb at them. Go on the flat rock in front of you, then on another one ahead, then twice to the left, to the top, towards the next room and go on north. Place a bomb next to the rocks on the rail tracks, then go left. Make a bomb roll towards the rocks in the middle of the tunnel, then another one towards the rocks at the back of the tunnel to blow them up as well. Then launch your Beetle at the Timeshift Stone to bring this place back to life. Backtrack a little and talk to the robot that informs you that one of his friends got abducted! Go towards the Timeshift Stone, go left, slash or avoid the hanging Deku Baba, and go ahead. Be careful with the next Deku Baba, jump ahead of you and open the chest containing a Blue Bird Feather or another rare treasure. Jump down, go to the cart and push it towards the time barrier to reach another area.
After Fi's explanations, place a bomb next to the rock on the right to reveal another Timeshift Stone! Strike it to bring the surroundings back to life, then climb the vines, go left, grab the ledge on the right and move left. Let go when you can see solid ground under your feet, then go ahead while looking to your right. Notice a kind of wheel half buried at the end of the track, jump towards the blue chest on the right to pick up another rare treasure, then turn around and go under the arch.
Go north while being careful because of the Ampilus. Climb on the huge flat rock from its west side, then open the chest to find a treasure called Tumbleweed. Fi says that you can catch them with a bug net. Take a look at the three cages, one of them containing a small robot. Get back to the chest, jump on the closest cage, then throw a bomb into the hole of the middle cage: another Timeshift Stone! Throw another bomb on the Timeshift Stone to activate it and bring the surroundings back to life, along with two Technoblins! Get out of the area to be out of range, shoot a nut with your Slingshot to stun them, then dash to them and quickly slash them. The cages' bars will disappear. Talk to the little robot that will notice your Beetle, and after a small operation, will upgrade it into a Hook Beetle! This artefact can now carry objects and drop them further!
Turn around and you will see a bomb on top of a tree... Launch the Beetle at this bomb to catch it automatically, then drop it into the bowl of a statue to make it fall. If you want to, you can get a blue rupee and do the same thing to the second statue to get another blue rupee. Go ahead to the south and do the same to the next three statues, then dash to the fallen statue, to the second one, and dash to the west. Go west again to another quicksands area. Throw your Beetle at the bomb atop the tree and drop it on the Ampilus. Then quickly run on its shell, then dash again straight ahead towards the flat rock. Fight off the Electro Spumes, then launch your Beetle again at a bomb and drop it on an Ampilus. Rush at its shell, get your breath back, then run northwest (still according to your map). Go ahead, take a look at the Bird Statue and save.
Look left, climb higher and go to the cart eastwards. Push it to create a shortcut then come back and jump towards the Goddess Cube. Perform the Skyward Strike, then use the Ampilus to get back to the Bird Statue. Launch the Beetle at the bomb on the cactus and drop it on another Ampilus. Rush onto its shell, get your breath back, then run to the next flat rock. Do the same with the Ampilus on your left, get on its shell, let it bring you to the northeast for a few seconds, then dash to the flat rock to the northeast. Run to the rock north, then to the arch north. Go ahead and get into the tunnel.