Once each of the three parties is standing on a switch in the Staging Area, they will be transported to a confrontation with Kefka. After both sides exchange dialogue, you will be prompted to determine an order for all of the Characters in all three parties. The first four Characters will make up your party for the first part of the four-part final battle. Each time you defeat the Monsters in a given part, each party member that is incapacitated will be removed and replaced with the next Character in order. If you don't have enough Characters left to fill the gaps, you will fight with whatever Characters survive in an abbreviated party.
Due to how these four battles play out, you are likely to have to replace at least one or two Characters at some point, so don't give all your equipment to your top four and ignore the rest. That said, you're not likely to get too far down the line, so you might want to redistribute your gear somewhat. You won't learn Spells or gain levels during these battles, so assign Espers based on which you plan to summon. Also, remember that there is no saving beyond this point, so there's no reason not to use all those Elixirs and even Megalixirs you no doubt have lying around collecting dust.
The first three parts of the final battle are different than most previous battles in that the enemies you're fighting have no names or graphics. Instead, you're essentially fighting invisible targets that correspond to background elements. Each of these battles contains multiple Monsters, and it is difficult to determine which one is responsible for any given attack. There is also no visual indication when one dies, though you will know that it has happened because the usual death sound plays (and that part is no longer targetable). In order to reference these nameless Monsters at all, I've given them the names used in the PlayStation Final Fantasy Anthology release.
Part One
The first battle is against a large humanoid torso with three segments: the Face, Long Arm, and Short Arm. Its right arm, in the front, is the Long Arm, and his left arm that is making a fist is the Short Arm. The order in which you fight the three parts of this foe can make the difference between a relatively easy battle and a potential party wipe. The Face and Short Arm become more aggressive at low HP, while the Long Arm will calm its attacks when weakened. In a similar vein, the Face and Long Arm will counter with powerful attacks if they are defeated last, while the Short Arm will not. This suggests an optimal order to the battle: Long Arm → Face → Short Arm. This is simple enough to remember, too. You start at the foreground and make your way back. If Locke is in the party (or Gogo is and can Steal), you can attempt to Steal an Elixir from each part. Due to their high levels (73–74), though, this can be difficult to pull off.
The Long Arm will use normal attacks and Shock Wave in relatively even amounts during the first phase of the battle. It has the most HP of the three with 33,000. Once you've dropped it to around 10,000 HP, it will cease using Shock Wave and stop attacking at all on 1/3 of its turns. The Long Arm makes no traditional counterattacks, but if defeated last, it will use Shock Wave up to three times before death. Both its basic attack and Shock Wave are reasonably powerful. It has a weakness to Wind, but does not resist any Elements.
The Face is the least active of the Monsters at the start of the battle. It will usually do nothing for the first four rounds, sometimes using R.Polarity to reverse the party's row setup or Slip Hit to cause Seizure. In the fifth round it will either cast Safe or Haste before resuming its usual lethargic action cycle. Once you've cut through 2/3 of its 30,000 HP, it will use Slip Hit more aggressively, occasionally interspersed with the Petrifying Dread. In the fifth turn of this sequence, it will sometimes use Magnitude8. Its most dangerous attack is Quake, but it will only cast this if it is the last part to fall during the battle. Don't let that happen.The Face is the only part with an easily exploitable weakness, to Fire.
Finally, the Short Arm has the simplest action cycle of the three. At first it will simply attack 2/3 of the time. It will also counter attacks at the same rate, and with the same basic attack. Of the three parts, its physical attacks are by far the most powerful. It has 27,000 HP to start, and after you've dealt 16,888 damage it will start using the 1.5× damage VacuumWave on turns where it previously would have done nothing, while still attacking normally otherwise. It offers no special death counterattack beyond the usual 2/3 chance of a basic hit. It has a weakness to Water.
Part Two
The battlefield layout of the second tier of the final battle is considerably more complicated than the first. There are four targets, though you would not likely be able to guess what they were without the targeting cursor. The large tiger head at the bottom right is, predictably, called Tiger. The blue humanoid sitting atop the Tiger is Hit. The humanoid posing on the left side of the area is Magic. Finally, the mechanical contraption in the middle is Tools. Two general notes apply here: first, you can once again Steal an Elixir from each Monster if you're so inclined. Second, do not use Quake in this battle. Tiger absorbs Earth damage, and the other three Monsters are Floating.
Hit is probably the least threatening of the four Monsters. It will attack each round with a fairly low-damage attack by late-game boss standards. It will use 10 Hits, which results in 10 consecutive attacks, upon death. This counterattack is used regardless of when it dies, so you may not want to leave Hit for last in case it defeats an important character on its way out. It has 28,000 HP, the second least of the Monsters here.
Tools has the least HP of the four with 24,000, and has an easily targeted weakness to Thunder. It uses several relatively weak MagiTek-type attacks including Tek Laser, Diffuser, and Atomic Ray. It can also use Grav Bomb or Missile to deal fractional HP damage. It may use Delta Hit on any third turn to inflict Petrify. This attack always hits, so only a Petrify-resistant Relic can block its effects. Once you've dropped it to a little less than half of its starting HP, it will replace Atomic Ray with the slightly more threatening Absolute 0, but otherwise keep making the same attacks. The loss of HP will also reset the counter on when it will use Delta Hit.
Tiger is an odd foe, spending half of its turns completely idle. It makes a serious attack with Flare Star, N. Cross, or S. Cross during its second turn, but won't do so again for another four turns after that. It will sometimes make a basic attack two turns after using an Ability. With 30,000 HP and vulnerability to Ice, it makes a juicy target, but it will get serious after you've dealt at least 18,480 damage to it. At that point it starts using Flare Star, N. Cross, or S. Cross on every one of its turns, sometimes adding in the Zombie-inflicting Doom Tusk immediately afterward. Once you start attacking Tiger, keep up the pressure until it falls.
Potentially the most dangerous Monster on this battlefield, as well as the toughest, is Magic. It has 41,000 HP, no Elemental weaknesses, and has access to almost half of the Spells in the game. It does have one exploitable weakness, however, which is that you can Mute it. Exactly which spells it can cast depends on its current HP total. It will start combat off with Haste, Haste2, or Imp. On it second turn it usually casts Fire 3 but may also cast Muddle, and on turn 3 it chooses between Poison, Drain, and Bio. This third Spell can be followed by up to two Dispels This pattern repeats as long as Magic remains near full HP.
After you've dealt at least 10,280 damage to Magic, it changes its Spell selection. It can cast Stop, Life 3, or Rflect in its first turn. Rflect is an interesting case, because every Monster present except Tiger is actually immune to it. It follows that up with Ice 3, Bolt 3, or Sleep, and finally Pearl, Flare, or Slow 2. After another 10,624 damage, offensive Spells become even more common. Possibilities include Bolt 3, Flare, Pearl, Fire 3, and Ice 2. It can also cast Mute in the first turn of its sequence or Rasp in the second. This will remain Magic's offensive pattern for the rest of the battle (unless it is healed).
As you continue to damage Magic, it will start countering your attacks. At 10,240 HP and below (30,760 cumulative damage), it can counter any attack with Quartr. Deal another 5,120 damage on top of that, and its Quartr counter can also include up to two Dispels. Whether you leave Magic for late in the battle, dealing with its default Spell selection, or try to defeat it up front, is up to you. Keep in mind that its Quartr counter can occur even on a fatal blow, so you may go into the next battle without having a chance to recover from it if you defeat Magic last.
Part Three
The third tier has only two enemies. The humanoid lying luxuriously in front is Sleep, while the woman's head behind him is Girl. Sleep will provide the offense, while Girl offers support. She will use Life 2 to revive Sleep (albeit at 9,999 HP) if you kill him first, so she should be your first target. She has only 9,999 HP but she absorbs all eight Elements. Non-Elemental Spells like Flare or physical attacks and special Commands are your best bet. You can try to steal a Ragnarok sword before defeating her. You can't keep it in the long term, but you can equip it to someone during this or the next fight. As long as Sleep is alive, she can use Pearl Wind every turn. She will sometimes also use Calmness to inflict Psyche.
Sleep can open the battle with W Wind or Merton (or if you're lucky, neither). His Merton deals around 1,500 damage to any Character without Fire protection, and can be a serious problem if you came into this battle at low HP. He'll follow up with either his powerful basic attack or Condemned, then repeat this sequence of two actions until you've dealt at least 29,760 damage to him. At that point he will exclusively attack with Meteo for around 1,300 Mag.Def-ignoring damage per character. He will also start countering most attacks with Meteo or Train, an Ability that always inflicts Dark and Mute to anyone who is not immune to those Statuses. You can steal a second Atma Weapon from Sleep.
To complicate things before Kefka, Sleep will use Calmness upon death. 1/3 of the time he'll do this twice. Unlike Girl's, his Calmness inflicts Wound. Anyone without Wound immunity or high enough MBlock% will be killed and replaced for the battle with Kefka himself.
Kefka
Kefka starts the battle by using Fallen One to reduce every party member's HP to 1. Respond quickly with healing, preferably a Megalixir. Kefka's main battle sequence covers six turns after Fallen One. He can use his brutal Havoc Wing special on any turn. He can also attack normally on the first, third, and fifth turns after Fallen One. He can instead use Fire 3 on the second turn, Ice 3 on the fourth, or Bolt 3 on the sixth. He can use Train to inflict Dark and Mute on the party on the second or fourth turn. Any action he takes is going to require a response, though he will have idle turns on occasion. If you haven't triggered his second phase after seven turns, he'll use Fallen One again and start over.
The first phase change in the battle with Kefka comes after you've dealt almost 30,000 damage. Kefka's laughing face will appear and he'll use Goner in the next turn. This is a non-Elemental magic attack that can't miss and deals significant damage, but is mitigated by Mag.Def. After Goner, he'll start taking double turns using Havoc Wing, Train, and Revenger. Revenger is similar to a multi-target Dispel, though it does not remove Slow, Stop, or Berserk. He'll also start countering some attacks with a basic hit or HyperDrive, a magic attack that deals over 3,000 damage and also causes Seizure.
When Kefka is down to 10,240 HP or less, he'll start using Ultima rather than HyperDrive in his counters. It will deal more than 2,000 damage per Character. At 7,680 HP, Kefka's laughing face will appear again and he once again sets up for Goner, which he follows with Meteor for around 1,000 damage to each Character. He cannot use counterattacks during this sequence, so hit him as hard as you can while you can avoid Ultima.
The good news is, Kefka's defenses are nothing to write home about. His Defense and Mag.Def are thoroughly mediocre, and his only Elemental resistance is immunity to Poison. You can steal a Megalixir from him if you need one. With only 62,000 HP, you can defeat Kefka relatively quickly with a powerful, focused attack. Some bad luck with his counters can result in a loss, but as long as you keep your HP up (and are high enough level to survive his best attacks), you should be able to win the day.
When Kefka is defeated, sit back and enjoy one of the great RPG endings of all time. The credits-like ending sequence will reference every Character, and will even change depending on whether you recruited them in the World of Ruin. In theory you could complete the game with just Celes, Edgar, and Setzer and get a rather uneventful ending.