Veterans of the series should recognize the uniqueness of Skyward Sword. Simply, it involves giant birds, Motion Plus sword-swinging, and plenty of air islands in contrast to the land islands of The Wind Waker. Although not the same Link, your job is to go to the source and close the Gates of Soul. But first, Skyloft needs help with the invasion. Like Ocarina of Time and Twilight Princess, you can only use Link in this level. The only good news is the sword fighting compared to Skyward Sword is much simpler and doesn't require motion controls at all.
Fi comes to battle
Depending on which version you have, you can unlock the Owl Statue first before heading inside the church for the cutscene. Fi knows you're not the same Link, but her job is to help in any way and for the first time, you'll see her in action. So protect her as she brings pumpkin soup to this giant flying orca? It makes sense in this world. Keep her away from Bokoblins with shields until she reaches her destination.
Volga's on fire!
As you battle and conquer bases, Volga will arrive, requiring you to knock him down until Volga himself is on fire (not literally; Volga can be very vengeful due to his pride). Don't go near him as he'll nail you down very easily.
Instead, run or use the ocarina to get to the giant fairy located on the map, on the east side by the church where you first found Fi. Also, Fi could be in danger so give her full health at fatal moments, indicated by a green circle. Once you activate the fountain, the giant fairy brings a very large bowl of pumpkin soup to the flying orca. Then the giant orca blows thunder on Volga, weakening him and giving you a chance to defeat him. Go back and defeat Volga to complete the level.
There is one more thing to take care of. Unlike the Skyward Sword boss battle, this one is much simpler and quicker with your sword. Once you locate him, just battle the way you did with Volga and if Ghirahim's weakpoint is shown by the circle, knock him out and he'll be over and done with.
After a thousand kills, go to the middle of the west side just between the checkpoint area and the base. You need a bomb to uncover that spider.