[2] The film is set 30 years after the events of Mobile Suit Gundam: Char's Counterattack and features an all-new cast of characters.

In the year UC 0123, the military arm of Cosmo Babylonia, the Crossbone Vanguard, attacks the Earth Federation colony Frontier IV.

[3] Student mechanic Seabook Arno and his friend Cecily Fairchild are caught in the middle of the fighting as the Federation garrison is quickly overwhelmed.

Cecily is taken to meet her real father, Carozzo, and grandfather, Meitzer, who both dream of overthrowing the corrupt Earth Federation and replacing it with a more just aristocracy.

Due to the confusion caused by the Crossbone Vanguard's surprise attack, the Space Ark is run by a barely experienced skeleton crew with no available pilots.

Seabook returns to Frontier I, where he is again forced by the Federation to help defend the colony against an impending attack by the Crossbone Vanguard.

Cecily is assigned the advanced Vigna Ghina mobile suit and accompanies the Crossbone Vanguard as they break into Frontier I.

Carozzo then arrives at Frontier I and deploys the Bugs, automated war machines designed to specifically hunt down humans.

Zabine arrives on the scene, but decides to spare Seabook and the Space Ark due to his disagreement over Carozzo's use of the Bugs and Rafflesia.

[citation needed] Yoshikazu Yasuhiko and Kunio Okawara returned to work on the film with Tomino to recreate the core team from the original Mobile Suit Gundam series.

Yasuhiko hadn't done anything aside from character designs after Mobile Suit Gundam, but he participated on the condition that he would get to help create the story like he did in the original.

The average size was brought down to about fifteen meters in Gundam F91, with Tomino explaining that it would be easier for when the mobile suits were made into model kits, as they would be more easily posed with equally scaled human figures and easier to build dioramas around,[8] the same reason he offered for another animation series he worked on, Aura Battler Dunbine.

The theme of Char's Counterattack involved Newtypes, but Gundam F91 chose to go with the easily relatable concept of "family problems" as its main focus, which also made it easier to understand for newer fans of the series.

They also had the voice actors re-dub the film, and finally released the "director's cut" on VHS as "Mobile Suit Gundam F91: The Complete Version".