"Mobile Suit Gundam Moon Crisis in U.C.0099" is set in the Universal Century timeline, specifically in the year 0099, a period marked by political instability and the lingering aftermath of previous conflicts. The story unfolds on the Moon, where tensions between Earth's ruling powers and the lunar colonies escalate into a full-scale crisis. The narrative centers on the struggle for autonomy by the lunar colonies, which have long been exploited for their resources and labor by Earth's Federation government.

The protagonist, Kael Armitage, is a young pilot from the lunar colony of Von Braun. Kael becomes embroiled in the conflict after his colony is attacked by a rogue faction of the Earth Federation, seeking to suppress the growing independence movement. Kael, initially a civilian engineer, is thrust into the role of a Mobile Suit pilot when he stumbles upon a prototype Gundam, the RX-99 Luna Gundam, designed specifically for lunar combat. The Gundam's advanced technology and adaptability make it a key asset in the fight against the Federation's forces.

The antagonist, Colonel Marcus Veylan, is a high-ranking Federation officer determined to maintain Earth's dominance over the colonies. Veylan commands a specialized task force equipped with cutting-edge Mobile Suits, including the formidable Gundam Eclipse, a rival to the Luna Gundam. Veylan's ruthless tactics and ideological conviction drive much of the conflict, as he views the lunar colonies' aspirations for independence as a direct threat to Earth's stability.

The story explores the complexities of war, loyalty, and identity. Kael is joined by a diverse group of allies, including Mira Solis, a skilled pilot and former Federation soldier disillusioned with Earth's policies, and Dr. Elias Trent, a scientist who developed the Luna Gundam and harbors secrets about its true purpose. As the conflict intensifies, Kael and his allies uncover a conspiracy within the Federation that threatens not only the lunar colonies but the entire balance of power in the Universal Century.

The narrative is driven by intense Mobile Suit battles, political intrigue, and personal struggles. Themes of sacrifice, the cost of war, and the quest for self-determination are central to the story. The lunar setting provides a unique backdrop, with low-gravity combat and the harsh realities of life on the Moon adding depth to the conflict. The series builds toward a climactic confrontation between Kael and Veylan, with the fate of the lunar colonies hanging in the balance.