The Trakovites are a small sect who disapprove of shaping because of the never-ending cycle it creates. Traditional Shaper focus is on hard work and study to learn the arts of Shaping and Magic to that end the cheapest skill trainers are either in Shaper strongholds or are sympathetic to the Shaper cause. The Shapers are on the offensive, pushing back against the Rebels and decimating the 'Human' part of the rebellion, fighting to reclaim the continent of Terrestria from Rebel hands. Player Character start as a rebel in this game, much unlike the other Geneforge versions. They believe that the shaper ways are wrong, especially the way they handle creations (though the drakons do the same to other creations seeming themselves as superior). The rebels are fighting for freedom from the Shapers. He was created by another Drakon named Easss, and has led the rebellion ever since the passing of the latter. The Rebels are led by a Drakon named Ghaldring. They set up camp in one of the southern peninsulas of Terrestia and from there, they could send assaults to attack Southforge Citadel. This fortress is named Southforge Citadel, and is hidden among the parts of the Forsaken Lands. The Shapers decided to attack one of the strongholds of the rebellion. Several rebels formed an outpost in Illya Province.

Most of the humans went south to the Forsaken Lands, while the Drakons went northward into Burwood Province. The human rebel army they faced was defeated in the ruins of Thornton, and the rebellion was cut in half. Eventually, they took over Illya Province, a division of Terrestia.

They poured in vast amounts of resources to take back the Eastern side. The Shapers, however, fought back against the growing numbers of the rebels. The original Shapers there were taken by surprise, and lost the Eastern half of their mainland. Drakons, and the lesser creatures started chaos all around.

Most of it spread south into the land known as Terrestia. After the rebellion started back in Geneforge 3, it quickly spread to other parts of the world.

Geneforge 5 character editor