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The series takes place in the year 2400, where the world is controlled by the "Solar System Alliance." The reason the Alliance was able to take control is because they wield mobile weapons. Those humanoid weapons use "Cyclonics" electric chips that convert the superpowers and wisdom bequeathed to mankind into interference power. These humanoid weapons which amplify their pilot's psychic powers are called "Titanic DOWLs," or just "DOWLs" (Defender Operated by Wired Linkage). DOWLs do not lose to other weapons, and are part of the Solar System Alliance's unit, "Sophia," who keep the world under the Alliance's thumb. However, this will soon change when two DOWL Masters—Aoi Saotome and Reine Ward Takajou—have a fateful meeting at a high school in an aerial city.
Third class citizen Hibiki from the male-only planet of Taraak sneaks aboard the extra large battleship Ikazuchi as a result of unusual circumstances. However, it comes under attack from the Magno’s Family pirates from the female-only planet of Majere! It is Hibiki’s first encounter with those who are said to ‘eat men’s innards’ but..
Universal Century 0088, in the last weeks of the struggle between the AEUG and the Titans, when a small group of elite Federal Forces officers stationed at the asteroid fortress Pezun revolt against the pro-AEUG Federation leadership. The rebels, led by Brave Cod, declare themselves the "New Desides" with the Titans' ideology of Earthnoid supremacy. To put down the rebellion, the Federation dispatches Task Force Alpha to Pezun equipped with the very latest advanced mobile suit hardware, including a handful of Gundams - the most powerful of which is the MSA-0011 S Gundam, piloted by 22 year-old pilot Ryou Roots.