"Mobile Suit Gundam F91" is set in the Universal Century timeline, 30 years after the events of "Char's Counterattack." The story begins with the Crossbone Vanguard, a militarized faction from the aristocratic Space Colony Frontier Side, launching a surprise attack on the Frontier IV colony. The Crossbone Vanguard, led by Iron Mask (Carozzo Ronah), seeks to establish a new aristocratic order by conquering Earth and its colonies. Their advanced mobile suits, including the titular Gundam F91, give them a significant military advantage.

The protagonist, Seabook Arno, is a civilian engineering student living on Frontier IV. When the colony is attacked, Seabook and his friends, including Cecily Fairchild, are forced to flee. During the chaos, Seabook discovers the Gundam F91, a prototype mobile suit developed by his mother, Monica Arno. Despite his lack of combat experience, Seabook pilots the Gundam to defend the colony and protect his loved ones. The Gundam F91's advanced systems, such as the Bio-Computer and VSBR (Variable Speed Beam Rifle), make it a formidable weapon against the Crossbone Vanguard.

Cecily Fairchild, Seabook's childhood friend, is revealed to be Berah Ronah, the granddaughter of Meitzer Ronah, the leader of the Crossbone Vanguard. This revelation creates a conflict of loyalty for Cecily, as she is torn between her family's ambitions and her bond with Seabook. Iron Mask, a ruthless and power-hungry figure, manipulates Cecily to further his goals, leading to a climactic confrontation between Seabook and the Crossbone Vanguard.

The narrative explores themes of war, identity, and the clash between idealism and authoritarianism. Seabook's journey from a reluctant civilian to a skilled pilot reflects the broader struggle of ordinary people caught in the crossfire of political and military conflicts. The story culminates in a decisive battle where Seabook confronts Iron Mask and the Crossbone Vanguard's forces, striving to protect his friends and prevent further destruction.

"Mobile Suit Gundam F91" is notable for its focus on character-driven drama within the larger context of a war-torn universe. The film condenses a complex narrative into a concise runtime, emphasizing the personal stakes of its characters while maintaining the franchise's signature blend of political intrigue and mecha action. The Gundam F91 itself serves as a symbol of hope and resistance against oppressive forces, embodying the series' recurring themes of technological advancement and human resilience.