Clearing areas by defeating guardians or successfully traversing the terrain allows players to bypass those areas via the world map, reducing travelling time. The first two areas serve as the game's tutorial introducing players to navigation, controls and shaping creations. The game world is divided up into 77 areas accessible through a world map. Geneforge is played in 45° axonometric perspective, movement through the game's environs is real-time but switches to turn-based combat in the game's playing field. Whilst searching for a way off the island, the game's ultimate goal, players can form alliances with the island's inhabitants and complete quests through combat or other means. Players create a character and travel around Sucia Island, a location Barred to the members of the player character's sect. The plot and setting were praised by reviewers for uniqueness and detail. Geneforge received a positive reception from reviewers, despite the quality of the graphics being rated as poor and the game containing one piece of music, the title theme. Sales exceeded the developer's expectations, despite fears that the departure from Spiderweb's Avernum series would deter players. Vogel had difficulties balancing gameplay with the powerful directed-energy weapons players would expect to use in a science fiction game. The game's setting, a mixture of science fiction and fantasy, differs from the pure science fiction setting the game had been envisioned as. The Shapers and the world of Geneforge were the result of Vogel imagining how would a being possess such power and how would they use it. The game's setting stemmed from the idea of players being able to create and control a group of obedient creatures.

The primary motivation of the player is to escape the island and, in the process, deal with the forces working to steal the Shaper secrets abandoned on Sucia Isle. The island contains groups of the Shapers' creations, who have formed their own ideologies regarding their creators in the intervening years.

The apprentice is cast away on Sucia, an island abandoned by the sect 200 years prior. Players assume the role of an apprentice Shaper, a sect of mages who can create living creatures through force of will. Geneforge is the first video game in the Geneforge series of role-playing video games created by Spiderweb Software.

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