Episode 3 of The Eminence in Shadow S2 begins with Claire and Mary continuing their search for Cid in the tower. They come across an empty coffin and wonder if Cid was meant to be a sacrifice for the Blood Queen.

On another front, Beta, a member of Shadow Garden, is reprimanded by her superiors for deviating from her primary mission: obtaining a blood sample from the Blood Queen Elisabeth. They make it clear that Shadow will handle the Blood Queen.

The Blood Queen awakens and begins absorbing the blood of her enemies, not only healing herself but also enhancing her powers. Beta and her team find themselves in a precarious situation, forced to fight against the queen's newfound abilities.

Claire, who is in terrible condition after an attack by the Blood Queen, encounters a mysterious figure named Aurora ("Witch of Calamity" from S1) in a dream-like state.

As tension rises, the Juggernaut of the Black Tower appears, interrupting the ongoing battles. He expresses his interest in fighting Shadow Garden, hinting at future conflicts.

While the Blood Queen grows stronger, Beta and her team find themselves in an increasingly desperate situation. They realize that Shadow has yet to appear, suggesting he may have a higher priority or a grand plan to fulfill first. This puts even more pressure on Beta to resolve the situation quickly, especially since Claire, the sister of their lord, is in critical condition.

Aurora, the enigmatic woman, continues her conversation with Claire, explaining that her body is trying to adapt to two different types of blood—that of the Possessed and that of the original vampires—and that Claire's symptoms stem from her inability to control her powers. These powers are going wild because the two blood types are trying to assimilate within her. Aurora heals Claire, helps her understand her condition, and teaches her how to control her abilities. She ultimately reveals that she is helping Claire because she belongs to Shadow.

Shadow finally appears and confronts the Blood Queen. His magical energy is so immense that he can stand against her. The episode reaches its climax as Shadow manages to stop the Blood Queen. Beta and her team are relieved and express their deep admiration for Shadow.

In a quiet moment, Cid and his sister discuss the unique powers manifesting in her left hand. Cid assures her that he will support her no matter what path she chooses. The episode ends with Cid pondering the lawless city as a potential source of income, referring to it as his "piggy bank."