"Mobile Suit Gundam F91" is set in the Universal Century timeline, 30 years after the events of "Char's Counterattack." The story unfolds in UC 0123, focusing on the conflict between the Earth Federation and the Crossbone Vanguard, a militaristic faction from the space colonies. The Crossbone Vanguard, led by Carozzo "Iron Mask" Ronah, seeks to establish a new aristocratic order by overthrowing the Earth Federation and asserting dominance over the colonies.

The protagonist, Seabook Arno, is a young engineering student living in the frontier colony of Frontier IV. His life takes a drastic turn when the Crossbone Vanguard launches a surprise attack on the colony. During the chaos, Seabook encounters the Gundam F91, a prototype mobile suit developed by the Earth Federation. Forced into the cockpit, Seabook becomes an unlikely pilot, defending his friends and family from the invading forces. His childhood friend, Cecily Fairchild, is revealed to be Berah Ronah, the granddaughter of Carozzo Ronah, and is manipulated into joining the Crossbone Vanguard as a figurehead.

As the conflict escalates, Seabook and his allies struggle to protect their colony while uncovering the true motives behind the Crossbone Vanguard's actions. The Gundam F91, equipped with advanced technology such as the Bio-Computer system and beam shield, becomes a key asset in their fight. Seabook's journey intertwines with Cecily's internal conflict as she grapples with her identity and loyalty, torn between her upbringing and her newfound role within the Crossbone Vanguard.

The narrative explores themes of war, identity, and the consequences of political ambition. Key battles, such as the defense of Frontier IV and the climactic confrontation with the Crossbone Vanguard's flagship, highlight the high stakes of the conflict. The story concludes with a resolution to the immediate threat, though the broader implications of the war and the characters' futures remain open-ended, reflecting the ongoing struggles within the Universal Century timeline.