The Missing Sister Quest is an optional side-quest in Skyward Sword where you can earn yourself an empty bottle. This quest is required to find all the Skyward Sword Bottle Locations. To start this quest, you must have finished the Skyward Sword Lost Child quest.
Anyways, this guide will walk you through the completion of the Missing Sister.
Missing Sister Quest
The first thing you will need to do is to talk to the man near the Light Tower. He will tell you that his sister has gone missing and he would like some help in locating her.
To locate her you will need to start flying in the direction towards Fun Fun Island. As you are doing so you should notice that there is a small island where a Loftwing has landed.
When you land you will see the man’s sister. Talk to her and she says she is in need of some medicine. So return to Skyloft and talk to her brother and he will give you Mushroom Spores inside of a brand spanking new empty bottle.
Return to the island where the girl is located and she will give you 5 Gratitude Crystals. However, that’s not it! Once the bird is healed you can get 5 more crystals by talking to the girl’s brother.