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Rune Factory: A Fantasy Harvest Moon has eight caves in total. All must be cleared in order to complete the storyline. This can take as many years as you want it to take. You can only enter the caves in order and you need a permit for each one. In order to get the permit for the next cave, you have to have defeated the boss of the previous cave.
In Rune Factory each cave has a unique climate that is perfect for growing certain crops, like a green house in Harvest Moon: Island of Happiness. Each cave also contains certain monsters that are perfect for collecting, if they do something useful.
The monsters in each cave are coming from the Monster Generators. Ivan gives you a Monster Generator radar when you first enter Carmite, so you can always see where they are. You must destroy the Monster Generators so it will stop producing monsters. Also, the Monster Generator will always be back if you leave and reenter the cave.
In order to get through the caves you need to take your time and upgrade your weapons. A sword is a must!
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Fighting in Rune Factory is real time and could be better if it weren't so clunky. You can choose from a variety of weapons to fight with, all of them upgradable by either buying a better one or crafting one yourself.
The basic weapons you can are: sword, spear, and lance. Gardening tools can be used as weapons, although they aren't as effective. You can even buy a staff and learn magic as your basic defense, although a mixture both magic and melee fighting is the most advantageous.
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This is the first cave in Rune Factory: A Fantasy Harvest Moon. Take your time getting through it, as it will be difficult at first.
Permit: Try to enter the cave. You can't. Talk to the mayor and he will give you the permit.
Carmite has 4 levels and 13 fields to plow.
Boss: Greater Daemon
This guy can be a bit hard if you don't have a good sword or aren't leveled up enough. Save your money and buy the best weapon you can afford. Avoid his swiping attacks and charging attacks. Hit him after he charges. Don't forget to fill a bottle with Edward's HP medicine!
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The second cave in Rune Factory. The monsters are getting harder.
Permit: Till 50 squares of land inside Carmite Cave. Defeat Carmite Cave boss.
Toros is an ice cave with few plots of land to till. However, there are several very big ones in the front of the cave.
Destroy all the Monster Generators on the first floor to unlock the door to the north of the entrance. Destroy all the Monster Generators in the cave to unlock the boss door.
Avoid his attacks by constantly running away from him and swinging your sword in his path. He'll stop while casting spells which is a perfect time to attack him.
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This is the third cave in Rune Factory.
Permit: Till 100 squares of land inside Toros Cave. Defeat Toros Cave boss. Talk to the mayor and he will not give you the permit, but he will ask you to talk to the people in town. Talk to everyone is town and find out that Cici is missing. Talk to the mayor again and he will give you the permit.
This summer cave is full of fire! In order to get passed it make sure you have plenty of water in your watering can (try to upgrade it as many times as you can before you enter).
This boss spits out Ants, so you'll have to defeat them when they get in the way. It's a giant plant that also casts different magic spells, but they are all location based and easily avoided. Just keep healing (if you have the medical spell) and attack it between castings and you should be able to defeat it.
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This is the fourth cave in Rune Factory.
Permit: Till 100 squares on land inside Clemens Cave and kill the boss. Talk to the mayor and he'll give you the permit.
The best thing about this cave is collecting Buffamoos as you will finally be able to produce milk with them. Finally, it's becoming more of a Harvest Moon game! Be sure to have plenty of monster huts ready back on your farm so you can collect them! You will also need a milker in order to collect the milk.
This dragon boss is pretty slow and easy to avoid, since all of its attacks are physical. Side step the fire breath, tail attack and slash attack and whack him with from behind to quickly take him out.
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Misty Bloom Cave
Misty Bloom is the fifth cave in Rune Factory. How many years did it take you to get here?
Permit: Till 100 squares on land inside Mt. Gigant and defeat the boss.
This cave is only accessible during the winter, as it is surrounded by water the rest of the year. Therefore, if you finish Mt. Gigant in spring, you will have to wait until winter to continue your quest. However, it does have some really good fishing spots, which is a plus for a Harvest Moon game.
This water monster has a whole pool to swim in, while you are trapped on a measly ring of land. Attack when she comes on land. Get behind her and hit her before she can attack and jump away. Try to hit her again before she jumps back into the water and you can kill her quickly (if you've leveled up enough).
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Rune Factory's sixth cave.
Permit: Till 100 squares on land inside of Misty Bloom Cave and defeat the boss.
These are the ruins Sharron is always standing in front of. There is something strange going on inside of them, much like the other caves in the area. Once inside, you will come to a locked door that says it will unlock once the earth is blessed. There is also a plot of land in the room. You have to till the soil and plant something there. Once the crops are ready to be picked the lock will open.
This rock giant is fast and has powerful attacks. Try to attack him from afar with a weapon that has a power up attack. Keep running away from him and charging your weapon to attack. Once you attack, run away again and repeat until he is defeated. Remember to heal!
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The seventh cave in Rune Factory's story mode.
Permit: Till 100 squares of land inside of Kasimir ruins.
There are more locked gates in this cave that require you to plant something to unlock it. There are strange tracks inside the cave and if you follow them you'll learn the truth about the Monster Generators and what has been going on for the past year or more.
Boss: Battle Tank
While it has a lot of HP, it is set on a track and easy to avoid. The attacks only come out of certain areas, but magic doesn't work well against it. Make sure you have a powerful weapon of some sort that is not magic to attack it with. You can easily stand next to it and hit it.
Once it has taken a lot of damage it will transform into another weapon, a beam gun. Just stand still and move right before it fires at you, then run up and hit it until it is defeated.
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The final cave in Rune Factory.
Permit: Once you have defeated Danaan Cave you can enter this cave. Talk to the mayor and he should give you the pass.
Greed Cave has a summer climate and is pretty straight forward. Once you destroy all of the Monster Generators inside of it, you will find a silver square on the lowest level. It looks like a save point. If you step on it you can be teleported to the boss.
This is the ultimate boss battle in the game, but if you are leveled up enough it shouldn't be too difficult. Avoid its lightening and fireball attacks by running away. It also has a light beam and gas breath attacks that need to be avoided. Stand in front of this dragon and hit it while avoiding the attacks that come out of its mouth and you should defeat it in no time.
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There is more to do in the caves in Rune Factory: A Fantasy Harvest Moon than just defeat the bosses.
Till the soil and plant as many crops as you can in certain caves. It will help you get through the cave by restoring your RP along the way. You don't have to water them or pick them for there to be a Rune Point there each day.
Leave other caves as wild as you can leave them for the plants that grow. Grasses of various colors can be used in medicine making.
Fish inside of the caves for special fish.