"Mobile Suit Zeta Gundam" is a sequel to the original "Mobile Suit Gundam" series, set in the Universal Century timeline. The story takes place seven years after the One Year War, during which the Earth Federation and the Principality of Zeon clashed in a devastating conflict. The Earth Federation has established the Titans, an elite task force, to suppress remnants of Zeon and maintain order. However, the Titans' authoritarian methods and brutal tactics spark widespread resentment, leading to the formation of the Anti-Earth Union Group (AEUG), a rebel faction opposing their tyranny.

The protagonist, Kamille Bidan, is a young and emotionally driven engineer living in the space colony Gryps. Kamille becomes entangled in the conflict after a confrontation with Titans officers, leading him to steal the prototype mobile suit, the Gundam Mk-II. This act draws him into the AEUG, where he joins forces with veterans like Quattro Bajeena (later revealed to be Char Aznable, a former Zeon ace pilot) and Bright Noa, a seasoned officer from the original war. Kamille pilots the advanced Zeta Gundam, a transformable mobile suit, and becomes a key figure in the AEUG's struggle against the Titans.

The narrative explores the escalating tensions between the Titans, the AEUG, and the remnants of Zeon, now reorganized as the Axis Zeon. The Titans, led by figures like Jamitov Hymen and Bask Om, employ increasingly oppressive measures, including the use of bio-engineered Cyber-Newtypes as weapons. The AEUG, meanwhile, seeks to dismantle the Titans' power and restore justice, though their methods and alliances are often morally ambiguous. Kamille's journey is marked by personal growth, as he grapples with the psychological toll of war, the loss of comrades, and the complexities of loyalty and identity.

Key characters include Emma Sheen, a Titans defector who becomes a trusted ally; Four Murasame, a Cyber-Newtype with a tragic connection to Kamille; and Haman Karn, the ambitious leader of Axis Zeon, who manipulates events to further her own agenda. The story culminates in a climactic battle at Gryps, where the AEUG and Axis Zeon clash with the Titans, resulting in significant losses and a shift in the balance of power.

Themes of political corruption, the ethics of warfare, and the psychological impact of conflict are central to the narrative. The series also delves into the concept of Newtypes, individuals with heightened spatial awareness and empathy, and their role in humanity's evolution. "Mobile Suit Zeta Gundam" is noted for its darker tone compared to its predecessor, with a focus on the moral ambiguities of war and the personal struggles of its characters.