Here is a boss guide for GS2. Hope it helps!
Section 1: Chest Beaters
Location: Kandorean Temple HP: 150 Drops: Nut EXP: ? Coins: ?
The Chest Beaters are the first boss that you will face in The Lost Age. These primates like to use health and status boosters frequently, so you can afford to let your characters get low on HP before healing them because it's unlikely that all three monkeys will attack. Plus, the monkeys only have about 150 Health Points, so they're a relatively easy kill. Have Felix's Echo Djinni on standby before the match so he can unleash a summon right away. Have Jenna use any of her multiple enemy attacking Psynergy and use Lightening with Sheba.
Section 2: King Scorpion
Location: Yampi Desert HP: 1050-1100 Drops: Vial, Scoop Gem EXP: 440 Coins: 228
King Scorpion is a reasonably tough boss. His attacks can do a lot of damage, so make sure to have your characters healed at all times. Come into the battle with all of your Djinn on Standby and unleash summons on him during the first series of attacks. From there, you should have Felix healing; Jenna Summoning, using the Fume Psynergy or using healing items such as Herbs or Nuts; Sheba should be using her Plasma Psynergy and occasionally using Djinn and Summons. The most important thing is not to let any of the characters die. Feel free to use Herbs throughout this match because you won't have much use for them after this point.
King Scorpion has a large amount of HP so don't expect any quick KO's.
Section 3: Briggs
Location: Alhafra
Briggs: HP: 1000 Sea Fighter: HP: 200
Drops: Vial EXP: ~689* Coins: ~1411*
*Depends on the number of Sea Fighters Briggs calls
This will be a very difficult fight if you went directly from Yampi Desert to Alhafra without going to Air's Rock yet. I suggest being at least Level 12 and having as many Djinn as possible or else this will be a very hard fight.
Despite there only being two pirates who confront you, you will have to fight up to three pirates. However, only Briggs poses any serious threat. Briggs has the ability to revive any of his fallen comrades, so focus your fire on him. Go into the battle with all of your Djinn on standby and unleash on them (make sure to always target the middle on as the primary pirate to hit.) Once you've finished the initial summoning, have Felix use Djinn as well as summon. Jenna should also use Cannon to allow Felix to use the Zagan Combination Summon. When Jenna is not using a Djinni, have her use her effective Fume Psynergy on Briggs. Sheba pretty much should use Plasma throughout the battle. However, it's not a bad idea to give her healing items as she's the strongest character and using Djinn frequently will reduce her maximum HP. Remember that the pirates are weak to every attack so it does not matter who is attacking, just make sure to use their strongest attack possible.
One thing to watch out for in this battle is the smaller pirate's strong sword attack that can do a lot of damage especially when both the Briggs and the supporting Sea Fighters attack the same character. Also watch out for the Oil Drop that the enemy uses frequently as that will do a large amount of damage to your entire party.
Once you kill the Briggs the other two will come down relatively easy. Just use strong Psynergy and attacking Djinn on them to take them down quickly.
Section 4: Bandits
Location: Outside Madra After Talking With Karst Note: Only avalible if you transfered data from Golden Sun in which you talked with the Mayor of Vault after Collosso
Bandit: HP: ~350 Thief: HP: ~200
Drops: Golden Boots EXP: 366 Coins: 521
This is one of the easier boss fights that you will face in the game. The Bandits are pretty much a pushover compared to some earlier and later bosses. All you need to do is unleash Psynergy on them and they will fall within a few turns. No character should ever be in danger of dieing.
Section 5: Aqua Hydra
Location: Your Ship HP: ~2750 Drops: Vial EXP: 963 Coins: 1612
Go in to the Aqua Hydra battle with all of your Djinn on Standby. This battle will be about blasting the Giant Squid with summons early. Initially, have all of the characters summon their straight Djinn summons (for example: Felix summons 3 Earth, Jenna 4 Fire, etc.) You should have at least 2 Level 4 Summons that should unleash between 500 and 800 damage a piece on Aqua Hydra.
After the first unleashing, Aqua Hydra will probably deal some serious damage on your characters since their stats will be low as the Djinn are recovering. In the second round you will probably want to heal with both Felix and Piers while Jenna uses her Fume Psynergy and Sheba uses her most powerful Lightening Psynergy. Once your characters are pretty much recovered, have Felix use Ragnarok; Jenna continue ot use her Fume Psynergy; Sheba alternate between using Impact on Felix or Jenna; and Piers should continue to heal whoever is damaged. You may want to occasionally have Felix or Jenna use Djinn to get some summons again.
Aqua Hydra does not really have any all powerful attacks so beating him should not be that much of a problem.
Section 6: Serpent
Location: Gaia Rock HP: ~3000-3500 Drops: Sand EXP: 1995 Coins: 2989
If you have not yet shone the four lights on the Serpent this battle will be literally impossible so I suggest that you go back and do that. Once the lights are shining on the Serpent, the battle still will be difficult. Go into the battle with everyone's Djinn on Standby except for all of Jenna's and Pier's Shade Djinni. Start the battle by unleashing Felix's, Sheba's and Pier's natural summons. Any Jupiter attack will be very effective on the Serpent while Venus attacks are not very effective. That being said, try to focus on unleashing Djinn and Summons with Sheba while Felix uses Ragnarok, Jenna heals and Piers alternates between setting and casting Shade. Sheba should be able to start doing summons that deal over 1,000 damage to the Serpent by her second summoning.
Just concentrate on keeping everyone alive throughout the battle. Heal with Felix rather than attacking if another character is low on HP. Watch out for the Serpent's Poison Breath attack that may poison several of your characters at once. Also, remember that the Serpent will heal 30 HP each turn. This isn't that big of a deal if you are unleashing summons for over 1,000 damage on him.
Section 7: Avimander
Location: Champa HP: ~4000 Drops: Potion EXP: 2176 Coins: 1330
Go into the battle with four Djinn on standby for Felix and Sheba. Jenna should have all of her Djinn set so that she can use Healing Aura throughout the battle. All of Pier's Djinn should be on standby since he is super effective against the Avimander. On the first turn, unleash summons with everyone except Jenna who should attack since her agility will be higher than the Avimander. From there, Felix should use Ragnarok, Jenna should use Healing Aura, Sheba should alternate between High Impact and Resist and Piers should use Djinn to build up another Summon. Once Piers unleashes his second summon it should do over 1,300 damage which will hurt the Avimander a great deal. The fight isn't that hard overall because the boss has no real devastating attacks.
Section 8: Poseidon
Location: The Sea of Time HP: 5000 Drops: Psy Crystal EXP: 2930 Coins: 3762
Go into the battle with 4 Sheba's Djinn on standby and all but 4 of Jenna's on Standby (which means you should put 2 on standby if you have all of the Djinn up to this point). Piers and Felix should have all of their Djinn set throughout this battle. Equip the Trident on Felix. Poseidon will not take any damage unless you use the Trident on him first. So, go into the battle using defense building and healing spells with everyone except Felix who should use the Trident item (note: Go to the items menu and use the Trident, don't actually attack). This will allow you to do damage to Poseidon and it will also do about 200-220 damage to him. So, continue to use the Trident with Felix throughout the match. Sheba should use Summons Poseidon for the second turn and then she should use Impact on Felix as well as Resist until your stats are maxed out at which time she should start using attacking Psynergy or Djinn. Jenna should use her Healing Aura spell when characters need healing, or unleash one of her Summons or attacking Djinn. Make sure to always keep 4 Mars Djinn set on her or else she will not be able to use Healing Aura. Piers should be using his Djinni Shade throughout the battle.
Poseidon attacks up to *three times* per turn, so be fanatical about keeping your party at perfect health. Make sure to keep four Venus Djinn set on Felix so that he can Revive and characters that fall. The best approach on Poseidon is the slow-but-steady approach.
Section 9: Moapa
Location: The end of Trial Road Moapa: HP: 3000 Knight: HP: 2000
Drops: Hover Jade EXP: 3340 Coins: 2870
Make sure that you configure your character before you start the race so that you do not waste valuable time. Felix, Sheba and Piers should all have atleast 4 Djinn on standby to unleash summons this round. Make sure that Piers has his Shade Djinni Set, though. Jenna should have 4 Djinn Set and the rest on Standby.
Unleash each character's appropriate summon (Felix would unleash 4 Earth, etc.) on the first turn while Jenna attacks or consider using Eclipse which will greatly drop the enemies' attack. The second turn, and from here on out, Jenna should use her whole party healing spell while Felix uses Ragnarok and Oddysee to pound on the two guards. Sheba should constantly use either Resist or High Impact. Piers should continue to use or set his Flash type Djinni each turn. Concentrate on knocking out Moapa first and this battle should be pretty easy.
Section 10: Agatio and Karst
You will only have two characters to fight Agatio and Karst with: Felix and Piers. Since you have so few party members, I recomend going into the battle with all of your Djinn Set to have the best Psynergy and stats. Have Felix and Piers use their Super Ragnarok and Super Ice Missile Psynergies (they should be the first on the list) respectively. After two series of attacks Jenna will join you in the battle. She should pretty much heal throughout the battle. Finally, after four series of attacks Sheba will join your party. She should use Djinn, Summons and powerful Psynergy against Agatio and Karst. Throughout the rest of the battle have Piers use his Flash-like Djinni while Felix continues to attack and use Super Ragnarok.
Keep your party at full heatlh throughout the battle as Agatio has a very powerful Tiger Psynergy similar to Jenna's and periodically they will attack with a Summon. Don't let Felix's PP get too low because Karst has an attack that will occasionally kill you in one shot, so you will need him to revive frequently. The battle shouldn't be too hard if you play conservatively. Agatio and Karst do not have many more points than the Indian Chief did.
Section 11: Mini-Dragons
The battle is not quite as hard as a boss battle but it still will be harder than a normal random battle. You will want to go into the battle with either Mia or Jenna healing while the other characters are unleashing summons and using Djinn. If any of your characters go do, you may want to sub in reserves using the option in between attack and retreat. The Dragons don't do too much damage so you shouldn't worry too much about having your characters faint. Focus on the small dragon first so that you will take less damage. After that, the larger dragon should fall pretty easily to some powerful Summons.
Section 12: Doom Dragon
The Doom Dragon is the boss of the game so you know that it is not going to be a walk in the park. Go in to the battle Isaac, Felix, Mia and Jenna. Everyone going into the battle should have their Djinn set while the people on reserve should have their Djinn on standby ready for summoning when they sub in. Hopefully you've been leveling everyone pretty equally so you won't have any particularily weak characters. Also, make sure that your characters are at full health before going into the battle by using leftover HP healing items. You will also want to distribute the healing items (especially party healing potions, Psy Crystals and Sacred Feathers) to characters who sub in so they can get you out of a tight spot. Place the Flash-like Djinni on Mia. Unforetunately, you will not have the Djinni Flash unless you transfered it from Golden Sun.
For as long as you can you will want to follow this strategy: Have Isaac and Felix both attack each turn. One of them should have the Trident and one of them should have the Sol Blade (you obtained this earlier in Mars Lighthouse). Mia should use her Flash-like Djinni (see a previous section for a description on what this Djinni's name is) each turn until it gets put to rest by the Doom Dragon's anti-Djinn Psynergy. Jenna should consistantly use her party healing Psynergy until she also cannot use it because of the anti-Djinni Psynergy. Hopefully either Mia and Jenna will always be able to use a class healing Psynergy.
Keep your characters at full health at all time because the Doom Dragon attacks four times per turn! Initially his attacks will not be very hard and won't do that much damage to you. However, as the battle goes on he will get progressively harder. About halfway through the battle the Doom Dragon will start using his Summon and even more annoying "Put All Your Djinn On Rest" Psynergy. This point occurs after it uses a bright yellow light on itself and appears to do no damage. It's extremely hard to defend against both the Anti-Djinni Psynergy and the Summon. However, try to keep Felix and Isaac both with a lot of spare PP so that they can revive freely. Also, be prepared for characters to just randomly faint apparently after some Psynergy that the Doom Dragon uses (I can't quite pinpoint which one). Plus, the Doom Dragon has an annoying Flash-like move that will reduce your damage to almost nothing.
You will probably start to get in a lot of trouble after the second out of the three dragon heads explode. Try letting the subs come in for a few turns using the Switch option next to Attack. Unleash their Summons on the first turn and then use Psynergy with them. Just try to hold on for as long as you can constantly trying to revive the healing characters while attacking with the non-healing characters.
The Doom Dragon has a lot of HP and the battle will take you a very long time so you may want to set aside some time to fight it.
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