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2017 a.t.b. (Revolutionary Year 228), the war between Euro Britannia and the European Union (E.U.) continues. At a disadvantage, the E.U. army founded a special team consisting of Elevens—exiled Japanese who had their country occupied by Britannia—known as the W-0 Unit; one of these Elevens, Akito Hyuga, fights with great agility and savagely executes the enemy while apparently under the power of Geass. Elsewhere, Military Advisor Julius Kingsley and Knight of Seven Suzaku Kururugi are traveling by train to St. Petersburg.

The new members of the W-0 unit attempt to desert, but this is prevented by Akito and Leila. The team (with Leila joining them) is then sent behind enemy lines to the city of Slonim, where they are ambushed by Euro Britannian forces led by Shin, Akito's brother. Akito, Leila, and the three Japanese recruits manage to survive, as a result of the BRS synchronization phenomenon. Meanwhile, Suzaku Kururugi and Julius Kingsley have arrived in St. Petersburg from the Britannian mainland.

After the W-0 unit is denied access to head back to headquarters, they come across a group of elder gypsies who temporarily take them in; as they get along well, Akito and Leila reveal what happened when they were children and thus leading them to where they are now. Meanwhile, Julius Kingsley, revealed to be a brainwashed and dark side version of Lelouch Lamperouge, expresses his form of control as several leaders look on in awe and disgust.

While W-0 is away, Leila and the remaining crew at base find themselves surrounded by Britannian Knightmares. Piloting the Vercingetorix, Shin Hyuuga leads the enemy charge, having usurped the position of Grand Master in the Knights of St. Michael. With her core members unavailable, it's up to Leila to protect her comrades, but this may be much tougher than she realizes: a spy lurking among them is finally ready to reveal himself. Left with no choice but to surrender, Leila arranges a meeting with Shin in order to ensure the safety of her squad. But as negotiations begin to fall apart, Akito and an unexpected ally return in the nick of time to turn things around.

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 Knights of St. Michael regroup in order to launch a final assault on Castle Weisswolf, the W-0, 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 their victory against Shin's troops, Akito, Leila and the other members of the Wyvern Squad retire. Shortly after, a young man named Rolo rescues Suzaku and Lelouch from the Euro Britannnian prison and informs them that Emperor Charles zi Britannia requests a new audience with Lelouch/Julius Kingsley.