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In UC 0093, the Federation has recovered from its defeat and has created a new anti-colonial special forces unit to deal with rebel forces: Londo Bell. Elsewhere in space, Char Aznable reappears out of self-imposed hiding with a declaration that he now commands his own Neo-Zeon movement, and intends to force the emigration of Earth's inhabitants to space by bringing about an apocalypse.
In the year Universal Century 0079, humans have colonized the area of space lying in between the Earth and the moon. However, the ambitious Zabi family, rulers of the Duchy of Zeon, the grouping of colonies furthest from the earth, has sparked a war.
The Ark Fleet has been destroyed, and a significant number of the enemy's troops have been wiped out due to its crash landing. As the remaining forces of the Holy Order of Michael regroup in order to launch a final assault on Weiswolf Castle, the wZERO unit, along with their new ally Ashley Ashra, stand ready to intercept them. Meanwhile, with his Geass out of control, Shin moves to erase his younger brother's existence once and for all. But Akito, having promised Leila that he will come back alive, refuses to accept such a fate, and the two clash in their final battle.
After discovering the face of their true enemy, someone who is related to Akito and responsible for the Geass placed upon him, W-0 attempts to return to their base at Castle Weisswolf. However, stranded in Warsaw due to a complication involving their military identification, they are forced to accept the help of local gypsies, allowing the squad to take some time to deepen their bonds. Meanwhile, Britannian advisor Julius Kingsley and his guard Suzaku Kururugi begin working together with the Knights of St. Michael in order to crush the European resistance once and for all, armed with the destructive power of a giant weapon known as the Ark Fleet.
12 years after Char's rebellion, Hathaway Noa leads an insurgency against Earth Federation, but meeting an enemy officer and a mysterious woman alters his fate.
Under constant attack by monstrous creatures called Angels that seek to eradicate humankind, U.N. Special Agency NERV introduces two new EVA pilots to help defend the city of Tokyo-3: the mysterious Makinami Mari Illustrous and the intense Asuka Langley Shikinami. Meanwhile, Gendo Ikari and SEELE proceed with a secret project that involves both Rei and Shinji.
