U.C. 0123. Mobile Suit Gundam F91 is Gundam creator Yoshiyuki Tomino's attempt to launch a new Gundam saga, set thirty years after Char's Counterattack. The story of Gundam F91 revolves around teenage space colonist Seabook Arno, his friend Cecily Fairchild, and the efforts of the Crossbone Vanguard militia, led by Cecily's grandfather Meitzer Ronah, to establish an aristocracy known as "Cosmo Babylonia". In keeping with Gundam tradition, the civilian Seabook is forced by circumstance to pilot the F91 Gundam, coincidentally designed in part by his estranged mother, Dr. Monica Arno.

In the future, with Earth's population rapidly increasing, humanity has developed giant orbiting space colonies gathered in clusters known as "Sides." As the elites on Earth force most of the populace into space, rebellion begins to brew. In the year Universal Century 0079, one of the colony clusters known as Side 3 declares itself the Principality of Zeon and launches a war of independence against the Earth Federation. Despite having only a fraction of the resources of the Federation, Zeon quickly gains the upper hand in the conflict through the use of giant humanoid robots called mobile suits. Chief among Zeon's mobile suit ace pilots is Char Aznable, a mysterious masked man known as the "Red Comet." When Char's squadron comes across the Federation developing its own prototype mobile suit called Gundam in the colony Side 7, his men launch a brutal attack. Amuro Ray, the son of the prototype's developer, gets in the Gundam and is able to fend off the Zeon attack. As Amuro soon finds himself directly in conflict with Char, he is forced to flee the colony on a Federation ship. [Written by MAL Rewrite]

The Federation space ship White Base and its precious cargo of prototype mobile suits have returned to Earth, only to find themselves in enemy territory. As the White Base struggles across the planet's surface to safety, Gundam pilot Amuro Ray must contend not only with the Principality of Zeon's fiercest warriors, but also with his own doubts and fears.

As the War continues, Amuro and the White Base crew must make their way toward the Earth Federation Headquarters, Jaburo. On there way they meet several new enemies and face off against impossible odds. They fight in Operation Odessa to releave the Earth from the clutches of the Zeon forces. Lives are lost, new friendships are made, and discoveries at ever corner. Amuro soon learns that he possess the powers of the mysterious Newtypes.