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...

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.