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This game follows in the footsteps of its predecessors with one screen showing a 3D view of the Wizardry-style dungeon, while the other one shows an overhead display of the map that players must maintain.
Like its predecessors, the game only partially maps the terrain for you. Players make use of a mapping system which lets them freely place icons on a gridded map. These navigation icons can represent sea currents, landmarks, and footnotes of the terrain that players encountered.
In Etrian Odyssey III, there are no pre-made playable characters. Players have to build their own guild by creating characters from a number of different character types (classes). Each class has its own skills and statistics, as well as limits on what equipment the character can wear. Although no more than five characters can be in the player's active party at the same time, up to 30 characters can be added to a guild, and players can switch out characters in town.
This third game in the series provides 12 all-new classes, as well as the ability to subclass (gaining most of the second class' skill set) with the exception of the unlockable class the droid that cannot be subclassed but can learn sub classes.
Another addition was the option to "set sail" on a ship that you are able to get after the first mission is completed. Your voyages depends on the amount of provisions that you have at the moment, restricting your movement only for the amount of spaces that the provisions allow you to advance. While at sea, the mapping system is the same as on the labyrinth, only with the addition of new navigation icons exclusive for sea mapping (e.g. whirlpools and islands). However, while sailing, there are no random encounters and no monsters except for pirate ships roaming the same ways as F.O.E.s on the labyrinth which, on contact, will sink your ship. Mission assignments for the player while on the sea will be to locate and reach foreign ports in order to restore armoroad's trading roads. Once a foreign port has been reached, a sea quest option will be available. The sea quest option will be to get rid of certain unique monsters that can only be found in that specific area, meaning that in order to complete the monster discovery book, the sea quest is mandatory.
Another addition not seen in the first two games is customizing weapons through forging. Forging is the act of including an effect in the weapon of your choice as long as the needed materials have been provided beforehand and the weapon has enough "sockets" or blank spaces to place the corresponding forge, along with the required money to pay for it. In order for this to be available, different "hammers" with the desired effects needs to be found either through quest or in chest located all over the labyrinth. The four categories to forge in to a weapon are: Bound (e.g. head bound, feet bound), Own Status (e.g. vitality, strength), Status Effect (e.g. poison, blind) and Element Attack (e.g. ice, fire).