The story takes place in Europe in the year a.t.b. 2017. A Knightmare unit made of boys and girls from Area Eleven are thrown into a military operation with a 5%chance of survival. They must rescue an allied unit left behind on the European warfront.

With her previous triumphs under her belt, Leila Malcal has now been promoted to Lieutenant Colonel and commanding officer of W-0. After having foiled an attempt to kidnap the General of the European army, she recruits the three perpetrators in order to make up for the lack of W-0's pilots. Ayano Kosaka, Yukiya Naruse, and ringleader Ryou Sayama accept, in hopes of finding a place to belong. When they are ordered to perform a commando raid by dropping into enemy lines, Leila decides to join them to prevent unnecessary casualties. As the unit rushes into the fight, Akito finds himself possessed by an uncontrollable lust for violence, slaughtering anyone that gets in his way. Little does he know, he is soon to come face to face with the one responsible for placing the bloodthirsty curse upon him, someone he is far too familiar with.

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.