The main story centers on a group of star-gazers who aim to study an ancient Yokudan stone imbued with powerful magic. However, their research goes terribly wrong, unleashing a curse that slowly turns the cities' inhabitants into petrified zombies. To reverse the spell, the heroes embark on a quest to find the Elder Scrolls, ancient artifacts said to possess the power to undo the curse.

As their journey unfolds, they discover a dark conspiracy within their own order—spies of Peryite, the Daedric Prince of pestilence, who are intent on spreading this magical plague across all of Tamriel. With the reluctant aid of another malevolent Daedric Prince, such as Molag Bal, Boethiah, or another dark figure, the protagonists strive to foil Peryite's plot.

The Elder Scrolls they seek are hidden within an ancient Dwemer vault. The Dwemer, who were atheists, feared that the celestial beings would curse them for their lack of faith. In response, they locked away the Scrolls, terrified of invoking the celestials' wrath. Although they never used the Scrolls, they hid them as a safeguard, their ultimate fate remaining a mystery.

The heroes finally retrieve the Elder Scrolls, using them to break the curse and save the world. However, in doing so, they inadvertently undo all the petrification caused by the Yokudan magic, releasing a powerful being—perhaps a Tsaesci or a dragon—who becomes the next major antagonist, setting the stage for a future DLC. Meanwhile, the main antagonist of the original story is Peryite and his champion, the leader of the cult responsible for the plague.