Several features of Zeta Gundam depart from the original series:

• The first Gundam series was initially about the personal lives of the main characters. Viewers gradually learned about the political landscape where the story took place. From the first episode, Zeta Gundam displays a major conflict between political and ideological factions.
• The Earth Federation's elite Titans task force emerge as the totalitarian parallel to what the Principality of Zeon was in the original show, contrary to the Federation's previous role in Mobile Suit Gundam. The Federation has become weak and corrupt under the control of the Titans' leaders. Consequently, alliances and affiliations shift: Amuro Ray, Bright Noa, Hayato Kobayashi, Kai Shiden, and Quattro Bajeena (Char Aznable) — former rivals from the previous series — now fight on the same side as the AEUG-Karaba alliance against the oppressive Titans.
• Char Aznable plays the role of mentor to new protagonist and lead character Kamille Bidan, effectively becoming the second lead character. This mentor-protege relationship plays a great role in shaping Kamille from an emotionally vulnerable, angst-ridden teenager to a true soldier. Kamille returns only three times in Zeta Gundam's direct sequel as he spends most of the series confined to a wheelchair due to his end of Zeta fight with Paptimus Scirocco.

Kamille Bidan is a troubled civilian youngster from Side 7's Green Noa 1 colony. His personal resentment towards the Titans results in him joining the AEUG. Quattro takes Kamille under his wings and becomes his mentor. The series also sees the partnership and cooperation between Kamille and Amuro, and the tension between Amuro and Char. Behind the frontline, the resistance group AEUG and Karaba are supported by many companies on Earth and in space, particularly the moon-based corporations. Besides financial support, the lunar manufacturing giant Anaheim Electronics also provides logistics and technical supports for AEUG, including spaceships, mobile suits, and munitions.

The series begins Quattro Bajeena raids the Titans military base in Green Noa 1 to acquire intelligence on a new mobile suit prototype, the "Black Gundams". Kamille, a hot-headed Newtype dissident, is caught up in the raid and helps AEUG steal the Mark-II. Eventually, he joins the AEUG, initially as the Mark-II pilot, then as the pilot of the new Ζ Gundam (made by Anaheim Electronics and based on Kamille's own design). Hayato Kobayashi and Amuro Ray meet up with them shortly after the AEUG descends on Earth to attack the Jaburo base but Amuro won't return to space. Both will stay on Earth with Karaba while Hayato's son, Katz, goes to space with Quattro.

Things are complicated further as Paptimus Scirocco, a "contract killer"/mobile suit developer from the Jupiter Energy Fleet (who, unbeknownst to his government handlers, is an extremely powerful Newtype) executes his own plan. He secretly conducts a coup d'état and takes over the Titans as part of his ambition to dominate the Earth Sphere. The war between Titans and AEUG will soon escalate as Haman Karn, the true leader of Axis Zeon, joins the war as well, leading to a three-way war. In the beginning, it is not clear which side the Axis Zeon is, as Haman's cunning plan is to play AEUG and Titans against each other and take advantage of the damage from the clash between them.