"The Eminence in Shadow" centers on Cid Kagenou, a young man obsessed with becoming a mastermind who operates from the shadows, manipulating events without recognition. Reincarnated into a fantasy world, Cid adopts the persona of Shadow, the leader of a secret organization called Shadow Garden, which he creates to combat a mysterious cult known as the Diabolos Cult. Unbeknownst to Cid, the cult and its connection to a supernatural affliction called the "Demon Possession" are real, and his fabricated stories inadvertently align with actual events.

Shadow Garden, initially formed as part of Cid's role-playing fantasy, becomes a legitimate force as its members, primarily women rescued from the Demon Possession, genuinely believe in his mission. Cid, however, remains oblivious to the gravity of the situation, treating everything as an elaborate game. His dual life as a seemingly ordinary student and the enigmatic Shadow creates a blend of comedy and action, as his over-the-top antics and misunderstandings often lead to unintended consequences.

The narrative explores themes of identity, power, and the blurred line between reality and fiction. Cid's unwavering commitment to his shadowy persona contrasts with the genuine struggles of those around him, particularly the members of Shadow Garden, who view him as a savior. The series balances its darker undertones with humor, often derived from Cid's exaggerated self-importance and the absurdity of his actions. Key characters include Alpha, the first member of Shadow Garden and Cid's most trusted ally, and Alexia Midgar, a princess whose interactions with Cid add complexity to the story. The plot unfolds through a mix of episodic adventures and overarching intrigue, as Shadow Garden's battles against the Diabolos Cult reveal deeper conspiracies and hidden truths about the world.