"Kiddy Grade" is set in a futuristic universe where humanity has expanded across the galaxy, governed by the Galactic Organization of Trade and Tariffs (GOTT). The organization employs a special division of agents known as ES (Encounter of Shadow-work) members, who are enhanced individuals with unique abilities. These agents handle sensitive missions, ranging from espionage to combat, to maintain order and protect the galaxy's economic and political stability.

The story centers on two primary characters: Éclair and Lumiere, a pair of ES agents working under GOTT. Éclair is a brash, impulsive fighter with superhuman strength, while Lumiere is calm, analytical, and possesses the ability to manipulate data and systems. Together, they form a highly effective team, balancing each other's strengths and weaknesses. Their partnership is tested as they uncover a conspiracy within GOTT that threatens the balance of power in the galaxy.

As the narrative progresses, Éclair and Lumiere discover that their memories and identities have been manipulated, revealing a deeper connection to the organization's dark secrets. The series explores themes of identity, loyalty, and the ethical implications of genetic and technological enhancements. The agents' missions gradually escalate in scale, leading to confrontations with powerful adversaries and revelations about their own origins.

The plot is structured around episodic missions that gradually build into a larger, interconnected storyline. Early episodes focus on establishing the world and the characters' roles within it, while later episodes delve into the overarching conspiracy and the personal stakes for Éclair and Lumiere. The series balances action, intrigue, and character development, culminating in a climactic resolution that addresses the central conflict and the fate of the galaxy.

"Kiddy Grade" features a diverse cast of supporting characters, including other ES agents, GOTT officials, and antagonists with their own motivations and abilities. The interplay between these characters adds depth to the narrative, highlighting the complexities of the political and social systems in the galaxy. The series maintains a steady pace, blending episodic storytelling with a serialized plot to keep the audience engaged throughout its run.