The story continues some time after the story in Heroes of Might and Magic V. Queen Isabel has returned to her empire, but the people speak of a changed queen, not the same one that went to Sheogh. Freyda, the daughter of Godric, is sent of to stop "rebels" as Queen Isabel calls them. Freyda is tasked to retrieve the young prince Andrei, and is sent on a chase to the home of the Dwarves, Tor-Hrall. There, Laszlo, Freyda's ally attacks the Dwarves while Freyda is at council with them. However, because of Wulfstan's kind heart, Freyda is let free. From this point on, Freyda no longer fights for her queen. She learns that her father has been kidnapped and rallies the help of Duncan, who assist her in getting a vessel to safely transport her to the empire.

The attack on Tor-Hrall leave the Dwarves slightly shaken. Wulfstan and his brother Rolf have opposing views, and thus Rolf allies himself with the Queen, while Wulfstan fights his own battles. As a result of this civil strife, Wulfstan ends up facing many Dwarves, however, plenty of those Dwarves tend to rally to his aid after realizing their own mistakes. As a result, Wulfstan's influence amongst the Dwarves grows. Eventually Wulfstan teams up with his friend Duncan and together they set a distraction to ensure the safety of Freyda's voyage. The city of Tor-Hrall is now recaptured in the name of Wulfstan. Soon after that, Laszlo is killed.

Ylaya is a Keeper of the Law and is told by the Daughter of Malassa to find out what rituals are being practiced by the Soulscar clan that do not heed Malassa herself. When Ylaya is discovered, she flees and seeks one who has been gone for many a month - Raelag. She finds him with Isabel and discovers that this Isabel is the real Isabel and the Queen is actually the succubus Biara, who has been spared on several occasions already. After making an alliance with Black Dragons, Ylaya brings down a great portion of the Soulscar clan, and the Dark Elf clans can thus be temporarily at peace. While that peace lasts, Ylaya and Raelag have one less enemy. Before the final battle, Raelag splits off from the group to achieve something that is to help in the war. Ylaya, Freyda, Duncan, Wulfstan and Isabel all meet up and combine forces to capture Tor-Hrall once and for all. King Tolghar is killed during the battle and the Empire's forces are seen retreating. After the climactic battle, it is revealed that Archbishop Alaric will still serve Biara. Raelag is seen talking with Tieru about something in the east and it is assumed that this is a direct reference to the Orcs, who are introduced in Tribes of the East.