Wutai Pagoda
You can complete the Wutai Pagoda side quest during Disc 1, Disc 2, or Disc 3; however, if you attempt to complete it on Disc 1 or 2, you will have to go through the process of having Yuffie steal your Materia and trying to get it back. Check out the Wutai side quest page for more information:
To begin the quest, travel to Wutai and make sure that you have Yuffie in your party. Read the Secret / Optional characters section if you do not yet have Yuffie as a member of your team. Travel to the Wutai Pagoda area near the back of Wutai, shown in the screenshot below.
Yuffie will undergo this trial alone, and she will face each of the upcoming opponents alone in battle. With that in mind, take some time to ensure that you have equipped her appropriately..
Some important Materia that you should equip her with includes the following:
Enemy Skill Materia with the “Big Guard” and “Aqualung” skills
Restore Materia- Poison Materia
Counter Attack Materia- HP Plus Materia
Make sure that you place her in the back row, as she is a ranged attacker who can still inflict maximum damage from the back row.
Godo’s Pagoda
Speak to the man and tell him that you would like to climb the Pagoda today. Your first fight is against the Sacred Gorky, listed in the game as Gorkii in the battle screen.
Note that the fights listed below may be much easier depending on what point in the game you attempt to complete the Wutai Pagoda.
Boss Battle
HP: 3,000
Drops: 
X-Potion
The strategy for most of these fights will be the same. Make sure to use “Big Guard” early on in the fight. Keep Yuffie’s HP replenished, as Gorky’s damaging spells will hit for quite a lot of HP. Gorky will use up his power fairly early on in the fight, so this is essentially a fight where you can outlast him.
Travel up to the next floor once the battle has concluded. Don’t forget to heal Yuffie up in preparation for her next fight. The next battle is against a young boy named Shake.
Boss Battle
HP: 4,000
Drops: Turbo Ether
Shake will put Yuffie under a status effect called Fury. Fury will cause Yuffie to take more damage, but it will also charge her Limit Breaks faster. It doesn’t take much to bring Shake down, but be prepared to heal Yuffie, as his attacks come pretty quickly.
Heal Yuffie up and have her equip the 
Jem Ring accessory (which you would have won off the Materia Keeper in Mount Nibel) in preparation for the next fight. Speak to Chekhov on the third floor to get the next battle started.
Boss Battle
HP: 5,000
Drops: Ice Ring
Chekov has very little HP, but his “Stare Down” move (which should be nullified by the Jem Ring) would usually delay Yuffie’s actions long enough to drag this fight out.
You can also use the Bio spell from your Poison Materia on Chekov, which causes him to take damage still, even if he manages to slow Yuffie’s actions.
TTravel up to the fourth floor once the battle with Chekov is complete. You don’t have to prepare for the fight against Staniv. Remember to remove your Jem Ring though if you equipped it in preparation for the last battle.
Boss Battle
HP: 6,000
Drops:
Elixir
Staniv will only use regular attacks, which makes this a breeze of a fight. Counter Attack Materia will help speed things up and make sure to keep Yuffie’s HP healed up.
Heal Yuffie up in preparation for the last fight and then head up to the fifth and final floor of the Pagoda. The fifth and final fight is against Yuffie’s father, Godo. Equip the White Cape accessory beforehand to prevent Godo from casting Mini/Small on Yuffie.
You should also equip each of the Enemy Skill Materia that you possess (assuming you have room for them), as Godo will cast an attack called “Trine,” which is pretty challenging to acquire. There is only one more point in the game where you will be able to obtain it.
Boss Battle
HP: 10,000
Drops: All Creation
Godo is a bit more complex of a fight. He uses gravity-based attacks, which drain a percentage of Yuffie’s HP. Be sure to keep her fully healed and to keep “Big Guard” up for the duration of the fight.
Once Godo’s health is below 40%, he will begin using Cure2 as a counterattack, which can make the battle extremely difficult if you are unable to deal more damage than he heals (~1200 HP). There are several options available to address this problem.
The first option is to rely on Counter Attack Materia to do the remaining damage to Godo each time he attacks you, as he will not counter a counterattack. You should also save up your Limit Breaks for the last half of the fight and use Bio or Bio2 from your Poison Materia on him early. Damage from Poison will not cause him to counter with Cure2 and is one of the most efficient sources of damage in this fight based on how much HP Godo has.
Focus on attacks that do the most damage, including “Aqualung” from your Enemy Skill Materia and Deathblow, to ensure that your attacks are either critical hits or are inflicting as much damage as possible without allowing him enough time to use Cure2.
Note that the Mini/Small status effect does not go away unless removed using a Cornucopia or a Remedy. The only alternative is to equip the White Cape accessory before the fight.
The battle against Godo is also one of the few places where you can learn the Enemy Skill called “Trine.” It is a good idea to have Yuffie equip one or all the Enemy Skill Materia that you possess during this fight.
The Wutai Pagoda side quest is now complete. Your rewards are the All Creation item, which you can use to teach Yuffie her Level 4 Limit Break when she has completed three other three levels, as well as the 
Leviathan Summon Materia.
Making Waves
Achievement/Trophy
You will obtain the 
Making Waves Achievement/Trophy automatically after you have defeated Godo and obtained the Leviathan Summon Materia as a reward.
Meet Your Maker
Achievement/Trophy
You will also receive the Meet Your Maker Achievement/Trophy once you teach Yuffie her Level 4 Limit Break, All Creation, using the All Creation item that Godo drops at the end of the battle.
Check out the Learning New Limit Breaks section for more information on how to teach your characters their strongest Limit Breaks.
You can return to the Side Quests section or back to the walkthrough section using either of the links below: