The year is Universal Century 0223. The Earth Federation has collapsed, and the space colonies, now calling themselves independent Settlements, have formed new political alliances. Two major factions have emerged from the ashes: the Congress of Settlement Nations, or CONSENT, which controls several Sides and their Earth-bound parent nations, and the Settlement Freedom League. CONSENT is facing a severe global food shortage, a crisis that threatens the stability of its power.

The story follows Mark Curran, an ex-CONSENT mobile suit pilot who has left his military past behind to work as a researcher at Hydro-Gen, an independent agricultural facility located in the Deep Face Trench on Earth. His quiet life is shattered when CONSENT forces, led by his former superior officer, the ruthless Lieutenant Colonel Jack Halle, storm the facility. They are hunting for intruders from the neutral Side 8 colony of Gaea. Mark rescues one of them, a young biologist named Cynthia Graves, from being executed by Halle, an act that makes him a fugitive.

Cynthia reveals that she possesses a revolutionary enzyme capable of allowing food to be grown underwater, a discovery that could end the global food crisis and break CONSENT's power. With CONSENT leadership, including the ambitious General Garneaux, determined to seize or destroy this technology to maintain control through selective starvation, Mark, Cynthia, her research interns, and Mark's jealous fiancée Mimi Devere, who is also a CONSENT intelligence officer, flee into space. Framed by Halle for murder, Mark seeks refuge with an old acquaintance, Philippe San Simeone, a member of the Illuminati, a private paramilitary organization resisting CONSENT. Philippe entrusts Mark with a powerful new prototype mobile suit, the G-Saviour.

The group arrives at Gaea, where Cynthia’s father is the Chief Councilor, just as a CONSENT fleet moves to attack. After a betrayal by Mimi, who hacks the colony’s defenses, Mark is forced to lead Gaea’s obsolete mobile suit force against the technologically superior Congressional Armed Forces. In the ensuing battle, Mark pilots the G-Saviour to duel Jack Halle in his advanced CAMS-13 MS-Rai, while General Garneaux reveals his true plan to destroy the enzyme sample and enforce mass starvation. The Illuminati fleet arrives to turn the tide of battle. In the final confrontation, Garneaux attempts to escape but is shot down, while a remorseful Mimi reveals she switched the enzyme sample, saving it. With Halle defeated and CONSENT forces in retreat, Gaea secures its independence, and Mark chooses to leave with Cynthia to bring the enzyme to Earth.