It is the year 2017, and Europe is being invaded by the forces of the Holy Britannian Empire. In an attempt to combat the opposition's overwhelming pressure and put an end to the massive casualties, the army forms a special unit called Wyvern, or W-0, composed of former Japanese citizens referred to as "Elevens." Recruited from ghettos, these young men and women pilot Knightmare frames—humanoid war machines—into dangerous operations where death awaits, hoping to make a name for themselves.

When a European regiment attempting to recapture a crucial city is pinned down by the enemy, it's up to W-0 to bail them out. Among those selected for the rescue operation is Lieutenant Akito Hyuuga, known as "Hannibal's Ghost" due to his prowess on the battlefield. However, the supposed rescue mission becomes suicidal when, in an attempt to take out as many Britannians as possible, the commanding officer initiates the Knightmare's self-destruct sequence. In its aftermath, Akito finds that he is the last one standing…

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.

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.