Veterans of the series should know the uniqueness of "Skyward Sword". Simply, it involves giant birds, motion plus sword swinging and lots of air islands in contrast to "The Windwaker". Although not the same Link, nevertheless, you're job is to go to the source and close "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 compare to "Skyward Sword" is much simpler and doesn't need motion control at all.
Fi comes to battle
Depending on which version you have, you can unlock the Owl Statue first before heading inside the church with the cutscene. Fi knows your 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'll bring pumpkin soup to this giant flying orca? It makes sense in this world. So keep her away from Boblokins with shields until she reaches her destination.
Volgia's on fire!
As you battle and conquer bases, Volgia will come out and he's burning hot! 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 in the map, next to the church where you first found Fi. Also, Fi could be in danger so give her full health at the fatal moment, indicated by a green circle. Once you activated the fountain, the giant fairy brings a very giant bowl of pumpkin soup to the flying orca. Then the giant orca blows thunder on Volgia, weakening him, and giving you a chance to defeat him. Go back and defeat Volgia to complete the level.
Girihim attacks!
There is one more thing. Unlike the "Skyward Sword" boss battle, this one is more simpler and quicker with your sword. Once you locate him, just battle the way you did with Volgia and if Girihim's weakpoint is shown by the circle, knock him out and he'll be over and done with.
Skulltulla location
After a thousand kills, go to the middle west side just between the checkpoint area and the base. You need a bomb to uncover that spider.