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For reference, the fanatic's tower is located on the Serpent Trench, closer to Nikeah (the head of the serpent) than to Mobliz (the tail). This is also where you pick up Strago in his sidequest. I would highly recommend that you teach at least one character Ultima before you attempt the tower, it will make things much easier going. Ultima can be learned either from the Ragnarok esper or the paladin shield, which is the uncursed "cursed shield." Both can be found in Locke's sidequest. I would also recommend purchasing wall rings from Thamasa, at the bottom right of the world map, and equipping them on all your characters. You will be unable to use anything but magic while in the fanatic's tower and you will earn no experience points, so keep that in mind when choosing your party, strong magic users are generally wise to pick, such as Terra, Celes, and Strago. Also make sure someone in your party knows Life 3 for the boss battle.

If one of your characters knows Ultima you can give them the Gold Hairpin or an economizer if you managed to steal one from an Aquila or win one from a brachosaur. It will do an unblockable magic attack to devastate the opposition. If you don't know Ultima or can't stomach the MP cost, simply cast a high level magic spell on all of your own party or an unblockable one on the opposite party. To restore MP during battles cast Osmose, or stock up on ethers.

The first door leads you to a Safety Bit, which prevents instant death spells. Step to the right of the chest and hit A to activate a secret door on the floor below, which gives you Edgar's final tool, the Air Anchor. Each level contains progressively harder monsters. The next level has a door leading to a Genji Shield, a very powerful shield. The next level contains a Stunner weapon for Shadow and the White Dragon. The White Dragon is vulnerable to mute. The dragon has no other weaknesses and casts holy/pearl magic. If you followed my strategy of equipping all wall rings most of the spells will just reflect and heal the dragon. The next level will give you the force armor, one of the best armors in the game which raises the all important mblock stat. Go up to the last level and enter the room at the top to get a Gem Box, which allows someone to cast two spells in turn. You will enter a boss battle upon leaving this room, and it is strongly recommend that you equip the Gem Box on somebody right away, preferably your strongest magic user. When you walk out, a bunch of Kefka's minions will surround you and you'll have to fight the Mage Master.

It is critical that you have at least one, and preferably all the members of your party protected by Life 3 at the end of this battle. Upon dying, the boss will cast Ultima which penetrates the defense of the Wall Ring and is likely to kill every party member. Hit the mage master with your most powerful spells, quick and the gem box will give you extra turns, and scan him or use unblockable spells to get around his wall changes. If you have Ultima in your repertoire this battle shouldn't be too bad. After you're done, you can warp out or simply trudge all the way back down and take off in your airship. You can bet the gem box for an economizer at the Collisium, which is a relic which reduces all spells to a casting cost of one, but I'd recommend holding onto the gem box since it is irreplaceable and you can win or steal Economizers in certain random battles.

• You can also cast Bersk on the final boss early on the battle, and then he will only perform weak physical attacks, no more wall changes, but he will still do the Ultima one when you kill him. This way you can beat him pretty quickly. It is also worth noting that, like nearly every monster in the game, he can be killed in one round by a high level fighter equipped with Atma Weapon, ValiantKnife, Genji Glove, and Offering. The caveat is that in this fight you must cast Bersk on your own character in order to trigger X Fight.
• Extra Note: For those of you who do not have Life3, or are unable to attain X Fight; here is a method that worked for me. Do not listen to the other skeptics that claim the battle would be otherwise un-winable, there is a way to win without all that fancy junk it just takes some thinking. Equip all 4 of your characters with Wall Rings and make sure one character has the Palidor esper equiped before the battle. Let the MagiMaster beat himself senseless with his own spells against you for a while, periodically using Scan to check his health. When he is at roughly 7 or 8k HP, hit him with Bserk. This will stop his aimless casting and his health is now able to be micromanaged by you. Hit him with a few strong spells until his health is around 1k, then hit him with weaker spells until his health is around 100-150. This may take some testing and fine tuning; but since he can't attack you powerfully, or finish himself off, you have all the time to test the damage of each characters spell while you take him down from 8k. Once his HP is within the range of 100-150, use the Palidor esper to initiate the jump attack. The first one or two to fall (sometimes the third) will usually kill him. He'll then cast Ultima. Since 1 or some of your other characters are skill in the sky, they will be unaffected by the spell and you'll survive the battle and win. It worked for me. It just goes to show, there's always a way if you take the time to think it out.