Go to Lanayru Desert and select the West Desert as your landing point. Go south-west, to the sand waterfall (again, sandfall?) and grapple your way inside. After talking to the Goron, roll a bomb into the small passage then crawl through.
On the other side, use the Beetle and the bomb flower on top of the cactus to blow away the rocks blocking your passage to the right. Jump over and go down, to where the boulder is. Use the Beetle to get the small key on the rock far down below, in the chasm (Look for sparkles). Once you have it, go back up and trough the locked door.
Grapple across the chasm and activate the timeshift stone in the minecart. Talk to the robot to get it moving and stand on the grass-obscured switch next to the door to open it. Follow the cart through the next room, the switch is again next to the door. Once outside, go across the platforms as they appear. When the cart approaches the door, vines will appear on the right side. The switch for the door is on top.
Follow the platforms as they appear once again. Once you reach the ledge with the Deku Baba, wait for vines to appear on the opposite wall and grapple there. Hit the switch, then continue on across platforms until some vines appear on the right wall. Grapple to them, and follow along, grabbing stamina fruit along the way and leaping across gaps. Once a platform appears underneath your feet, drop down, and look to the left side - there is a grappling point. Wait for the cart to approach it so it activates, then pull yourself to it, and then to the one opposite of it to reach the switch.
The next section is a grappling section. All the points are places in a zig-zag fashion and are easy to spot. At the end a vine patch will appear above the exit. Pull yourself there and drop down. Follow the cart through this corridor, fighting enemies as you go along. Be careful though, one wrong swing and you can deactivate the timeshfit stone on the cart - and sink into the sand. When you reach the gate use the whip to activate the lever and proceed. This is followed by two graps you have to swing across using the whip. Stop when you reach the electrified gate, wait for the cart to pass, then quickly sprint up the sand while grabbing the stamina fruit. Once up, pull the lever to continue.
Go across this room fighting enemies as you go along. The lever to open the door is behind the Beamos on the left, you'll have to use a whip. In the last section jump across the platforms as they appear. When the minecart stops use your Beetle to grab a bomb flower and break the stone. Continue along the path, killing the Deku Baba as you go.
Talk to the dragon after it revives. Head east, to the dead tree. Blow away the sand hiding the timeshift stone and activate it. Pick up the seed then head back. You'll have to use the Beetle to reactivate the timestone on the cart to get back across. Head to the Sealed Grounds now, and thorugh the Gate of Time. Plant the seed into the soil on the left and head back to the present. Roll into the tree and pick up the fruit. Now head back to Lanayru and choose Lanayru Gorge as your landing spot. Talk to the dragon to receive the second part of the Hero Song.