Dark Ages II is the story of three thieves struggling to survive in a world fighting against the descent into chaos. In short, this is the world of Engel over 500 years after setting of the first game. It has been drastically transformed by magical energies that have destroyed central authority. All that remains are small city-states and keeps run by feudal lords in a struggle to unite the fragmented countryside. Some have good intentions, others have different intentions. Within this power-struggle guilds have formed for the protection of citizens who share certain beliefs. Some are to protect honor, some to pursue knowledge. However, some are for power and profit. Chief among these is The Rein, a fanatic group that actively hunts and kills mages under the false beliefs they are the cause of the chaos in the land.

The three main characters are Syven, Xatar, and Povin. They are three apprentices to the Thieves' Guild, a guild that tries to maintain neutrality in the struggles of Engel, preferring to offer its services to the higgest bidder. Although all three characters are thieves, only Syven is a natural thief. Guild membership is determined by shared ideals, not profession. As such, the guild employs warriors, such as Xatar, and mages, such as Povin.

You begin playing the game during a routine assignment for the three apprentices. However, things go awry, and what should be routine becomes a mystery that must be solved to survive.