"Mobile Suit Zeta Gundam" is set in the Universal Century timeline, seven years after the events of "Mobile Suit Gundam." The Earth Federation has established the Titans, an elite task force, to suppress anti-Federation movements. However, the Titans' authoritarian methods, including brutal crackdowns on space colonies, lead to widespread resentment. In response, the Anti-Earth Union Group (AEUG) emerges as a resistance force opposing the Titans' tyranny.

The protagonist, Kamille Bidan, is a young and hotheaded civilian living in the space colony Gryps. After a confrontation with Titans officers, Kamille impulsively steals the AEUG's prototype mobile suit, the Gundam Mk-II, and becomes embroiled in the conflict. The AEUG, led by former Earth Federation officer Quattro Bajeena (later revealed to be Char Aznable), recognizes Kamille's potential as a pilot and recruits him. Kamille's journey intertwines with the broader struggle between the AEUG and the Titans, as well as his personal growth and relationships with other characters.

The AEUG's efforts to dismantle the Titans escalate into a full-scale war, with pivotal battles taking place across Earth and space. The Titans, under the leadership of Jamitov Hymem and later Paptimus Scirocco, deploy advanced mobile suits and ruthless tactics to maintain control. Meanwhile, the AEUG gains support from various factions, including the Karaba, an Earth-based resistance group. The conflict reaches its climax during the Gryps War, a series of intense battles centered around the Gryps 2 colony laser, a superweapon capable of devastating entire fleets.

Key characters include Kamille, whose idealism and determination drive much of the narrative; Quattro Bajeena, a seasoned pilot and mentor figure; Emma Sheen, a former Titans officer who defects to the AEUG; and Reccoa Londe, a conflicted pilot torn between loyalty and personal desires. The series also explores the motivations of antagonists like Scirocco, whose manipulative nature and ambition make him a formidable adversary.

Themes of war, political corruption, and the psychological toll of conflict are central to the story. Kamille's evolution from a brash teenager to a mature leader reflects the broader struggle for justice and freedom. The series concludes with a decisive battle that reshapes the balance of power in the Universal Century, leaving lasting consequences for its characters and the world they inhabit.