"Mobile Suit Gundam: The Witch from Mercury - Prologue" serves as an introductory piece to the larger narrative of the "Witch from Mercury" series, setting the stage for its themes and conflicts. The story begins in the year A.S. 122, within a futuristic society where humanity has expanded into space, and corporations wield significant power over interplanetary affairs. The prologue centers on the Vanadis Institute, a research organization developing advanced mobile suits, and the mysterious Gundam technology, which is powered by a system known as the GUND Format. This system allows pilots to synchronize with their mobile suits at a neural level, but it carries severe risks, including physical and mental strain on the user.

The protagonist, Elnora Samaya, is a skilled pilot and researcher at Vanadis. She is deeply involved in the development of the GUND Format, driven by a desire to create a safer future for humanity. However, her work attracts the attention of powerful corporate entities, particularly the Delling Group, which views the GUND Format as a threat to its dominance. Tensions escalate when the Delling Group launches a military assault on the Vanadis Institute, aiming to seize control of the Gundam technology. During the attack, Elnora's daughter, Ericht Samaya, becomes a key figure as she demonstrates an extraordinary ability to interface with the GUND Format, hinting at her potential significance in the unfolding conflict.

The prologue concludes with the destruction of the Vanadis Institute and the apparent death of Elnora, leaving Ericht's fate uncertain. The narrative establishes the central conflict between corporate greed and the ethical implications of advanced technology, while also introducing themes of sacrifice, resilience, and the human cost of progress. The prologue effectively sets the tone for the series, laying the groundwork for the struggles and moral dilemmas that will shape the story moving forward.