As the player completes tasks and defeats enemies they receive experience, leading to increased levels and additional skill points.

The skill "Anatomy", which allowed the player to cause extra damage in melee combat, is replaced with "Parry", which has a chance of blocking incoming attacks.

[3] The gates of Drypeak are found unmanned, much to Shanti's disgust,[8] the Agent and her charge are also attacked by rogue Shaper creations.

She instructs the apprentice, who is not guarded, to explore Drypeak and beyond in order to discover the truth behind the colony and Barzahl's disappearance.

[5][14] After exploring a number of the game's locations, the apprentice gains access to a guarded tunnel and is astonished to discover what lies on the other side.

[15] Whereas the valley where Drypeak is located is a dustbowl devoid of vegetation,[16] the lands on the other side of the tunnel are lush and green, meaning highly illegal shaping is taking place in secret.

[18] While still reeling from the revelation of what lies beyond Drypeak, the Shaper apprentice discovers that Shanti has disappeared during one of her escapes from her armed escorts, her necklace lay broken on the grass outside the tunnel.

[3] When confronted with the apprentice's findings, Zakary confesses to being part of a plot to conceal illegal experiments from the Shaper Council.

[26] Zakary pledges his loyalty to the Shaper Council once more and asks for help from the apprentice in dealing with what lies beyond the guarded cave.

[28] Barzahl cut off contact with Drypeak, preparing to repel the inevitable assault of the Shaper Council, who they wish to remain independent from.

[32] Trade and communications between Zakary's now Shaper Council loyalist Drypeak and the other three factions have ceased, replaced with spies and subterfuge.

The player is free to decide which faction they wish to join, if any, and to explore the game world, reacting to the characters and situations they encounter.

Due to the different reactions the player receives from the factions, depending on their actions and conversation choices, it required days to complete a single town.

The reviewer of Computer Games Magazine praised the Spiderweb Software's titles and said that Geneforge 2 "is probably the best twenty-five bucks an RPG fiend can spend".

[5] The game's graphics and sound effects received a largely negative response, Matt Peckham of GameSpy described them as "yesteryear" and "minimalist" respectively.

[3] Ken Newquist called the graphics "far from spectacular" and stated they were worse than older titles such as Baldur's Gate.

Newquist also disliked the ambient sounds, which make up the game's soundtrack, calling them "numerous, but repetitive".