Spoiler warning! This section of the article contains spoilers, or hints about the game's storyline or progression.
You might want to skip down to the next heading if you do not want facts about the game's storyline or plot revealed to you.
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This battle isn’t too hard if your party is strong. It attacks fast, so you might want to have Marle cast Haste on everybody. But it is not necessary. Make sure you have either a lot of Heals in your inventory, or have status protecting armor, because this mutant casts Chaos frequently. Take out the top half first, then go for the bottom half, and you should do fine.
The Giga Mutant is much more powerful than the Mega Mutant. It's immune to physical attacks including multi-element attacks that have a physical side to them (Bubble Hit, for example). Thus, you'll have to rely on all magic attacks and magic triple attacks (the Deltas, Poyozo Dance which you won't have the first time through, Ayla's Tailspin, etc.). This means that Magus and the Marle/Lucca combo are a pretty good choice (Antipode 3 for example), however you won't have a problem with any combo in particular. Whenever it uses Life Shaver, heal immediately because it will target a random ally soon after; thus you have a good chance of dying.
Remember to use a shelter at the previous save point after beating him!
The final Mutant boss on the Black Omen. This one drains the life from the bottom half and heals the top half; so at least it helps with the fight. The bottom absorbs magic damage and will counter with Life Shaver if attacked with a physical type attack and the top is highly resistant to physical attacks like the Giga Mutant. There are two methods to beating him, the fast way and the slow way. The fast way is to simply cast your most powerful magic spells over and over, such as Luminaire. The slow way is to wait for it to kill the bottom half while you take damage and heal yourself. Note that when the top dies, so will the bottom, but not the other way around.
The Lavos Spawn is just like the others but more powerful. Although it deals more damage and has more HP, it has better items to be charmed and it pays out a better reward. Like the first ones you encountered, don't attack the shell and don't use multi-target techs (such as Lighting2, Falcon Hit, Ice Water, etc.). Focus completely on the head and use your strongest attacks (i.e. triple/dual techs). Once the head is destroyed, the shell will die after a few seconds but note that if attacked it will still retaliate.
The queen is a fairly easy boss; she reduces your party's HP to 1 at the start of the fight and periodically casts the spell again and again. Simply use a lapis or a party heal technique to counter it. The fight will only go on for a little while so remember to charm her for some extra MegaElixers.
The remains of the Mammon Machine, now fused with Queen Zeal will become an active vessel for her to fight you with. It will begin the fight by noting that it "Modifies all energy"; thus what you do to it, it will counter and increase its defenses against. By attacking with physical, it increases defense, by attacking with a technique, it increases its attack power. It will release stored energy periodically and attack your characters with other attacks. A pretty easy fight, just use your most powerful attacks since its defense enhancing ability doesn't really affect you (it will have no affect against 3D Attack).
Queen Zeal will summon you atop the Black Omen, she'll curse you and then transform into this three piece avatar. Note that by targeting the hands at all you'll be paying a lot, even if you try and charm them. Also note that the right hand has a charmable Prism Helm, and the left hand has a PrismDress! Other than messing with charms, its an easy fight. Just focus on the head and heal up when needed. Remember to heal up after the head casts Hallation, otherwise you may end up in a pickle. Anything will save you, even a lapis. Destroying the head will bring the whole Zeal trio down.
An easy way to get past Lavos' Attack Modes and outer shell is to use the Flying Epoch to crash through it (set the time gauge to 1999 AD). You won't even have to fight this form of Lavos, however if you're going for the NewGame+ feature, you will have to face the shell at the end of the Black Omen.
Lavos' outer shell goes through many different "attack modes", featuring the attacks from previous bosses you have fought. Just remember the strategies you used for those bosses and use them to defeat Lavos each time. Each form is as strong as you first fought it so the first boss you face, the Dragon Tank, should only take 1-2 hits per element (the side aliens and Lavos himself).
The modes Lavos goes through are:
After all of the attack modes, you'll have to defeat the shell of Lavos for real.
The boss as you've seen before, although toned down a lot since the Ocean Palace fight. He deals less damage, has less HP and should be quite easy at the end of the game. He will begin the fight with Destruction rains from the heavens! and then continue with just Chaotic Zones and Needle Spins. Make sure you remove all chaos status ailments from your party as soon as they are inflicted with them. Heal often, and pound Lavos with your most powerful attacks.
Again with three parts (hands/head), he'll begin the fight with the Laser Beams attack. Take out the arms (right or left) first, then the head. Always heal and remove the chaos affects caused by Obstacle. Not much different than what you've experienced so far.
Interestingly, trigger abilities such as Lavos core shuts off defense, Lavos core defense restored! and Time warp... can all be counterattacked by Rage Band or Frenzy Band's effect despite dealing no damage to anything.
This battle is very complex, so you have to understand your enemy before attempting to kill it. It works like this: there are three bits, but the middle bit looks like a humanoid. This should make you believe that he's the main target, but he isn't. In fact, it's the right bit that you need to focus on destroying. Once you take it out, you defeat Lavos. The only problem here is that the right bit's physical and magic defense is maxed at the start of the fight. Also, the left bit constantly heals, while absorbing magic attacks (however it can't withstand more than a few physical attacks).
A suggested minimum level for this fight is 45. With a lot of practice, it's not hard to solo Lavos with any character at level 55+.
When one bit goes down, the right bit will shortly lower its defense to charge up "Active Life". This move completely revives all destroyed bits. After that, the right bit's defense will soon return to maximum, so you have to repeat the process. Sound simple enough? Well, it would be if it wasn't for the MIDDLE bit. This main body likes to warp in time a lot, and each time it does it acquires a devastating new attack. These include the most powerful magic and physical attacks in the game, which can kill your entire full-HP party in one hit if you're unlucky.
In spite of that, this can be an easy battle if you know what to do. Start with the bit on the left. Crono's Confuse, Frog's Leap Slash, Robo's Uzzi Punch, or Ayla's Triple Kick will take it out (or a combination of two). Don't even worry about the Middle Bit unless you know it's about to unleash an "Ultimate" attack (in which case you'll want to prepare healing). The bit on the right is what you need to destroy. Use all of your most powerful attack once it lowers its defense. One thing to notice is that techniques that are amplified by low HP, such as Frog Squash and Dino Tail, will hit all bits for a lot of damage. Just after reviving a character, such as when he/she has 50 HP, you can deal out about 2000 physical damage.
Lavos can cough up some brutal attacks (both magic and physical), so make sure you have someone who can heal well, or have plenty of MegaElixirs handy in your inventory. Eventually the destroyed bits will be restored. The left bit can heal the middle bit, so destroy it and go back to the "Active Life" bit. Once you've destroyed the bit, you've beaten the game. Now sit back and enjoy the ending!!