"Mobile Suit Gundam: The Witch from Mercury" is set in a futuristic world where humanity has expanded into space, with corporations and factions vying for power through the development and control of advanced mobile suits. The story centers on Suletta Mercury, a young girl from the remote planet of Mercury, who enrolls at the Asticassia School of Technology, a prestigious institution where students train to pilot mobile suits and engage in corporate-sponsored duels. Suletta is accompanied by her unique mobile suit, the Gundam Aerial, which possesses advanced capabilities and a mysterious connection to her past.

At Asticassia, Suletta becomes entangled in the complex political and social dynamics of the school, which serves as a microcosm of the broader power struggles between corporations and factions. Her arrival disrupts the status quo, particularly when she forms a bond with Miorine Rembran, the daughter of a powerful corporate leader. Miorine, who is initially reluctant to engage with others, finds herself drawn to Suletta's determination and kindness. Their relationship becomes a focal point of the narrative, as they navigate the challenges posed by rival students, corporate intrigue, and the ethical dilemmas surrounding the use of Gundam technology.

The series explores themes of identity, autonomy, and the consequences of technological advancement. Suletta's journey is marked by her struggle to understand her own origins and the true nature of the Gundam Aerial, which is revealed to be tied to a controversial and dangerous technology known as the GUND Format. This technology, which allows for a deeper connection between pilots and their mobile suits, is both a source of immense power and a potential threat to humanity. As Suletta uncovers the secrets of her past, she must confront the moral implications of her actions and the role she plays in the larger conflict.

The narrative is driven by a mix of personal drama, political maneuvering, and intense mobile suit battles. The corporate factions, including the dominant Benerit Group, seek to exploit the GUND Format for their own gain, while others view it as a means to achieve greater equality and freedom. Suletta's choices and alliances have far-reaching consequences, as she becomes a symbol of hope for some and a target for others. The series balances its exploration of these themes with action-packed sequences and character-driven storytelling, creating a compelling and multifaceted narrative.