You can do Yuffie’s side quest as soon as you get the Tiny Bronco, but can only do it in Disc 1 or 2. Go to the western-most continent and if you are in the Tiny Bronco, go to the far south of the island, and dismount on the beach. Head north and you will find a curving path that takes you up to the high mountain. As you reach the top, you will enter a plain and Yuffie will appear, and some Shinra guards will attack you. They are easy to beat and when you have defeated them, your party will realise that Yuffie has stolen all your materia. If you try to board the vehicle you won’t be able to as your party (if you have Yuffie in your team, Barret will take her place) will refuse to and want to go after Yuffie, so head north over the bridges and through the valley until you reach Wutai.
When you enter, you will see Yuffie run away. Head to the top left corner and go to the next screen. Head into the building to the right. You can rest in the room here, then go along the hall until you see a room with a man lying down inside. Go talk to him continually until he stands up and Yuffie will arrive, you will find out the man is Yuffie’s father, Godo. If you follow Yuffie, she will have disappeared, so go into the room next to the one with Godo in. Examine the right wall and a secret passageway will appear. At the end is a chest with a Hairpin in.
Go into the bar on the first screen and you’ll see the Turks, Reno, Rude and Elena. Talk to them and then go to the Item Shop. There is a chest that is normally blocked to the right, but you can now open it to get a MP Absorb materia. But just as you get it, Yuffie will drop down and steal it off you. Now go into the house to the south east of the town. There is a folding cover to the left. Examine it to find Yuffie. She will run away again. Go to outside the bar. You will see the pot outside moving. Examine it and the rest of your party will block the exits. Hit O 3 times to hit the pot and make Yuffie jump out. She will try and escape but will be stopped by your team. Seeing he has no other choice, she leads you to her house to give you back your materia.
You will see a scene where two Shinra guards will talk to the Turks at the bar. After this ends, you will be in Yuffie’s house. Follow her downstairs and talk to her. Examine the levers at the back, it doesn’t matter which one you choose, a cage will fall on your other party members, trapping them. After she leaves, examine the levers again to free your friends.
Go back to where Godo was, but don’t enter the building. There is an arch to the left, go through it and examine the bell her to ring it. This will reveal an entrance below. Go through it to see who has taken Yuffie….Don Corneo. He will also have nabbed Elena. Get the Swift Bolt and Elixer in the chests before going up the stairs. Three Shinra soldiers will attack you, kill them and find that the Don has escaped.
Go outside and talk to Reno and Rude. Go to the north east part of Wutai, where there are lots of paths in a mountain. Talk to the Turks and take the path that goes to the north. Go past Rude and go south to find the Don. He will summon a monster for you to fight…
As you probably don’t have any materia you can only attack. It’s a good idea to use some of the attack items, like Swift Bolt etc to inflict more damage, and use Hi-Potions etc to cure. You’ll win a Peace Ring.
Don Corneo will talk for a while and ask a question, answer however. Reno and Rude will turn up and kill the Don. You will return to Yuffie’s house where she will give you your materia back, but she will place it all wrong so re-equip it how you want.