"Mobile Suit Gundam: Char's Counterattack" is a manga adaptation of the 1988 anime film of the same name, serving as a pivotal conclusion to the long-standing rivalry between Amuro Ray and Char Aznable within the Universal Century timeline. The story is set in U.C. 0093, years after the events of the One Year War and the Gryps Conflict. Char, now the leader of Neo Zeon, resurfaces with a radical plan to force humanity's migration into space by dropping the asteroid Fifth Luna onto Earth, causing catastrophic environmental damage. His goal is to accelerate human evolution by forcing survivors to adapt to life in space, free from Earth's gravity.

Amuro Ray, now a seasoned pilot and member of the Earth Federation's Londo Bell task force, opposes Char's plan. The conflict escalates as Char deploys the powerful mobile suit Sazabi and later the massive asteroid Axis, which he aims to crash into Earth. Amuro pilots the advanced RX-93 ν Gundam, equipped with psycho-frame technology, to confront Char. The narrative explores their ideological clash, with Char advocating for humanity's forced evolution and Amuro striving to protect Earth and its inhabitants.

Key supporting characters include Quess Paraya, a young Newtype caught in the conflict, and Hathaway Noa, the son of Bright Noa, who becomes entangled in the war. The story delves into themes of Newtype abilities, the psychological toll of war, and the moral complexities of leadership. The climax features a dramatic battle between Amuro and Char, culminating in a final confrontation that leaves their fates ambiguous. The manga retains the core narrative of the film while expanding on character motivations and the broader implications of their actions, providing a detailed exploration of the Universal Century's most iconic rivalry.