The explorer starts off as a novice who must enter the Basic Certification Exam before allowed to work and explore the far reaches of Amostra by the Explorer's Union headed by Cid. S/he is equipped with a Crystalyzer which allows him or her to trigger a Crystal Surge and enter a Trance. After passing other aptitude exams, the explorer will be able to change his/her jobs. This enables them to take up a variety of Quests set up by different parties in Amostra. This includes opening up new areas for exploration, as well as defeating eidolons that can be found around the island.
The main aim of the Explorers' Union of which the explorer is a member is to open up a pathway to the Grand Crystal, and to remain neutral despite the backdrop of diplomatic tensions between the Lillium Kingdom, the Gartian Empire and the nation of Querasua, and the religious conflict between the Madulas Church and the Navarean Church. The Explorers' Union has also initiated a joint project with the RJDP Corp in their research into Crystalyzers.
Upon initiation, the player is prompted to choose their explorer avatar's gender and appearance. Players can customize voice, skin tone, face, eye color, and hair style and color. These features can be changed later in the Makeover option in the Main Menu, however, changing the gender of the avatar costs 10,000 gil.
The explorer can equip different types of equipment on their right and left hand, head, torso, legs and accessory. Certain outfits are only available to one gender and some are full-bodied outfits that will block changes to equipment on other body parts. Weapons affect Physical Attack and Accuracy, and Magical Attack, Recovery and Accuracy. Head, torso and leg equipment affect the Physical Defense and Evasion as well as Magical Defense and Evasion. Accessories may carry Equipment Traits such as Maximum HP or Elemental Resistance.
An explorer may equip as much as eight abilities based on their limitations set by the job they choose. Explorers can change a job only at Libertas, where all their equipment and abilities set will be removed. The chosen jobs also determine the type of equipment they can use. Different jobs have different base stats in HP, AP and Load. HP and AP are the typical hit points and ability points for health and ability usage. Load determines the number of ally monsters an explorer can bring in their Quests.
Once the Monster Lab is open, the explorer can bring an atmalith captured from a defeated monster to bring to the lab for monster creation. Once created, this ally monster can brought along in Quests, with a maximum number of three at one time.