The game has an always-visible auto-map, which begins each area completely darkened, and is revealed as the player explores. As the player's party performs tasks or defeats enemies they receive experience, leading to increased levels and additional skill points. The player character's skill points can be used to increase their statistics or to improve their aptitude in one of the fifteen available skills. Canisters which increase skills or add new abilities are scattered throughout the game.
Before starting the game, players choose from three basic character classes, each of which has a particular playing style. Guardians are fighters who excel in standard combat skills, especially hand-to-hand fighting. They are capable of shaping creations, but have little affinity for magic. Agents excel in spell casting and are capable of hand-to-hand combat, but have poor shaping skills. The Shaper is a summoner, capable of creating living creatures by using their own life essence. Shapers rely on their creations for protection. Every character class is referred to as "Shaper" in-game. Most objectives in the game must be completed via combat or diplomacy, but players can also use subterfuge to pass obstacles. All three character classes can use different methods, depending on which skills they are adept in. Some areas are difficult to pass, and some tasks are difficult to complete, unless the player character is a certain class. Each character class has a different combat style, the combat skills they are associated with cost fewer skill points to increase.
Essence is used for both creating creatures and casting spells; the number, type and strength of creations is limited by the player's essence capacity. For instance, if a character with 70 maximum essence summons a creature which costs 20 essence, their maximum essence is reduced to 50 until the creation is destroyed, either through combat or being absorbed by the Shaper to regain essence. A total of 18 different creations are featured in the game, with larger and more powerful creatures costing more essence to create. The types and strengths of creations can be altered depending on the player's combat style. Creations accompanying the player receive a percentage of the experience points received for completing quests or defeating foes, levelling up and receiving skill points in the same manner as the player character. These skill points can be spent to increase creations' statistics, but every statistic increase costs more essence and reduces the amount of essence available to summon other creations or cast spells. Essence and health are regained from Shaper-designed pools or by entering a friendly town.
Combat is turn-based, with each character in the player's party receiving action points at the beginning of the player's turn. The number received is dependent on the items the player character has equipped and the skills the character or creations possess. Each action uses a specific number of points, for example, moving one square takes a single point and attacks or spells take five. Attacking or spellcasting with fewer than ten action points immediately ends the character's turn, otherwise a character can continue to act until they run out of points. Most enemies will attack the player on sight, retreating in terror if they reach a certain threshold of damage without being killed. Other specialized behaviors are also present, including creatures which call for help, or creatures which act as sentries and retreat to an ambush location when threatened. Creations made by the player character can also be controlled by a similar artificial intelligence, or the player can invest more essence in the creation's intelligence and control them manually.
Geneforge's dialogue is delivered through on-screen text. Encounters with intelligent creations or humans result in the player being given a series of pre-determined questions or responses. Conversation options and the outcome of those conversations change according to the player's previous interactions. as well as which quests have been completed; which items the player has; which group the player belongs to and the player's leadership skill. The player can collect items from defeated enemies and the game environments to improve their own equipment. Non-player characters can trade with the player, buying most items regardless of type. The shopkeeper has a fixed amount of gold at the start of the game which does not replenish itself. It is possible for the player to drain all shopkeepers of their gold reserves, making it impossible to sell further items.
Plot
The player begins as an initiate of a powerful sect of magicians, the Shapers. Members of the sect create living beings from the magical essence within themselves. Apprentices are sent to academies to learn the art of shaping and the player's character has been accepted to do so. The player departs on a voyage to the academy aboard a specially modified Drayk, a dragon-like Shaper Creation. During the journey, the Shaper passes a group of islands, one of which is recognized as the Barred Sucia Island. Locations Barred by the Shapers are closed to both the sect and outsiders alike, meaning a catastrophe has occurred or something very valuable is located there. As the Shaper examines Sucia, lost in thought, the craft is attacked and mortally wounded by an unidentified sailing ship. After igniting the vessel's sails with a fireball, the craft deposits the Shaper on an abandoned dockside before dying. The player is now stranded on Sucia Island and must find a way to leave.
Exploration of the docks reveals a strange canister filled with swirling liquid. Thinking the canister contains healing or energizing properties, the Shaper breaks the seal and absorbs the contents. Instead the contents absorb into the Shaper's body, strengthening and changing it. The changes become visibly apparent, the player character's skin smoothens and glows slightly. The canisters also affect the user's mental state, causing a more violent and arrogant temperament. Serviles remain on the island, having been abandoned when the island was Barred. They are intelligent creations of Shapers, designed to serve them without question or hesitation. These Serviles have had no contact with Shapers for two centuries, and have separated into three groups with differing philosophies regarding their creators. The Obeyers are still faithful to the Shapers, the Awakened believe that they should be treated as equals. The Takers have rejected Shapers completely and view the sect as oppressors to be fought.