While the player can complete quests and form alliances with the island's sects (the Awakened, the Obeyers and the Takers), the ultimate goal is escape; it's possible to remain unaligned, even destroy the sects completely, and still succeed.
The player begins as an initiate of a powerful sect of magicians, the Shapers. Members of the sect create living beings out of magic and raw organic material known as essence. Apprentices are sent to academies to learn the art of Shaping; you play as one such apprentice.
The player departs on a voyage to the academy aboard a specially modified Drayk, a Shaper creation. During the journey, the Shaper passes a group of islands, one of which is marked on their map as Barred: Sucia Island. Locations Barred by the Shapers are closed to both those within the sect and outsiders alike, and often means that a catastrophe has occurred or something very valuable is located there. As the Shaper examines Sucia, lost in thought, the craft is attacked by an unidentified sailing ship. The Shaped craft they are on is mortally wounded during the attack, but manages to retaliate by setting the other ship's sails alight. It deposits the Shaper on an abandoned dockside before dying, taking most of their belongings down to the depths with it. The player is now stranded on Sucia Island and must find a way to escape.
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 them, and even allowing them to use magic without training. The Shaper uses their newfound abilities and whatever gear they can scavenge from the ruins of the island to fight past the rogue creations in their path and proceed deeper into the island's interior.
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.
After encountering the three servile groups, the player begins to learn of a group of foreigners known as Sholai, explorers who have been shipwrecked on the island. It was the Sholai, led by a man named Trajkov, who attacked the player with their last remaining ship. Trajkov controls a device called the Geneforge, created by the Shapers, which can rewrite the user's DNA and make them incredibly powerful. This is the cause of the island's Barred status, as the device was deemed too dangerous in the wrong hands. Trajkov and his followers have allied themselves with the Takers, using hundreds of the canisters and trying to claim Shaper powers as their own. The group was initially unable to activate the Geneforge itself, due to a Shaper being needed to activate the device. A Shaper named Goettsch was kidnapped for this purpose, in the same manner as the player-character, but Goettsch fled and stole the shaping gloves needed to safely use the Geneforge. Trajkov, rather than assault Goettsch's stronghold, attempted to kidnap the player as a replacement. During these events, some Sholai have escaped from their increasingly violent and unpredictable leader, and taken refuge in some of Sucia Island's caves.
Trajkov can be killed through combat or tricked into killing himself by using the Geneforge. He can also be aided in activating the device, if the player steals the Shaper gloves from Goettsch. Goettsch offers the player fake Shaper gauntlets, which do not protect Trajkov from the Geneforge's energy should he be convinced they are genuine Shaping gloves. There are also a pair of damaged Shaping gloves that can be found, which cause a similarly gruesome death should they be used.
The player is free to join any one of the servile groups, or remain unaligned. Geneforge can be completed without joining any group. In a similar fashion, the player can either assist Trajkov in claiming the Geneforge for himself, destroy it so nobody can use it, or even make use of its powers themselves. In any case, when the player escapes by using the boat moored in a guarded dock on the far side of Sucia Island, the game ends. Finishing the game unlocks one of more than a dozen game endings, dependent on the player's actions during the game.
A turn based game, Geneforge is divided into 77 different areas accessible through the world map when the player's character leaves a zone.
A list of zones and maps is accessible on the wiki here, here  and here. Areas, depicted in red, will not permit you to fast travel through them until explored or otherwise cleared; they are hostile. Areas colored green are generally not hostile, unless the character engages in theft, killing pets, or murdering intelligent beings. Towns, unless angered, allow the character and their creations to rest and restore energy and health. Essence levels are restored in town as well. Characters may be neutral, allied or hostile depending on your alliances and or leadership skills and magic (Terror & Dominate).