[Location: Earth, Earth's Atmosphere]

The year is U.C. 0105. Twelve years have passed since the end of the second Neo Zeon War (Char’s Rebellion). Even after “the Axis Shock,” which seemed to indicate the future of humanity and the Universal Century, the world is still in a chaotic situation where intermittent military conflicts continue to break out. The Earth Federation government is more corrupt than ever, and its leadership has not only accelerated Earth's pollution, but also implemented an inhuman "Man Hunting" policy in which civilians are forcibly exiled to outer space.

The anti-Federation government organization “Mafty,” led by someone called “Mafty Navue Erin," has taken a stand against the corruption of the Earth Sphere. Mafty carries out fierce acts of terrorism, assassinating high officials of the Federation government one after another, but it gains a certain level of support from the populace who are growing more opposed to the Federation government.

The one who goes by "Mafty" and leads the organization of the same name, is you. With help of your comrades, you launched into satellite orbit using a Galcezon sub-flight system equipped with a rocket booster to retrieve your new Mobile Suit. The Earth Federation forces, the Circe Unit, deployed the RX-104FF Penelope with it's pilot Lane Aime. Meanwhile, you change your pilot suits and jump into the Cargo Pisa, removing the cover inside to reveal... A Gundam.

Lane spots the descending Cargo Pisa and orders his team to intercept it. You boot up the Gundam while the heat of re-entry is about to burn up Cargo Pisa. Hit by one of the Penelope's beams, you flash back through the events of the last few days and hear the voice of Amuro Ray.

More of the Penelope's beams hit Cargo Pisa, Hathaway must get out or else the Valiant will be caught up in it, too. The Penelope is descending headfirst and matches the velocity of Cargo Pisa. Lane and Gawman see the mysterious Gundam climbing out of it and boost off into the sky. The Penelope fires two simultaneous shots from its shoulder-mounted Mega Particle Cannons, but to Lane's surprise, the mysterious Gundam dodges them.

In the stormy skies where beam shots fly, Mafty's spirit of rebellion strikes against the federation... With the Xi Gundam.