It's been one year since the failure of the Black Rebellion and the supposed death of Zero. Britannia has assigned Area 11 a "correctional education" status, where Elevens are made an example of by brute force, to try to prevent any future uprisings and suppress rebellious thoughts. Unsuspecting high school student Lelouch, oblivious to his rebellious past as Zero, stumbles upon a scheme on his life and the life of a mysterious woman known as C.C., who reveals to him his forgotten purpose and his "true" self. Destroying his assailants and declaring himself Zero once again, Lelouch sets out to finish what he started.
Naota is a normal Japanese 6th grade boy (although a little cynical), but when his older brother leaves for America to play baseball, his brother leaves his 17 year old girlfriend Mamimi behind. Mamimi is sending mixed signals and advances to Naota, and he doesn't know what to do about her. But to make matters worse, Naota's world is totally turned upside down when he is run over by a woman on a Vespa. During their first encounter, she hits him over the head with her guitar, which then causes a horn to grow out of his forehead. She calls herself "Haruko" and her presence changes Naota's life to even further insanity.
Noriko Takaya's dream is to become a space pilot like her father, Admiral Yuzo Takaya. He died when she was still a little girl due to an attack of alien forces in deep space. After entering Okinawa Girls Space Pilot High School, Noriko is handpicked by instructor Kouichiro Ohta as someone with great potential. She must then persuade everyone, especially herself, that she can indeed fulfill her goal and become an accomplished pilot despite being just an ordinary girl.
In an age when large-scale natural disasters frequently happen all over the world, when cyborgs and autonomous robots are beginning to appear on the market in technologically advanced nations, and major world powers compete for technology and resources, the divide between rich and poor grows and the future for the poor looks bleak. In this transitional stage, everyone wanders around in a self-indulgent daze and the way out isn't clear… This is the story of how two cybernetically enhanced girls meet.
Jr., the heir of Romana and his battle sabers Cherry and Lime, who have girl circuits are enjoying their peaceful life in Romana. Suddenly, the evil Star-Face and his sexadolls attack Romana in order to take over so Star-Face can become the next High Official. In order to truly become the next High Official and ruler of Romana, he must first eliminate Jr. This begins a battle for, not only Jr.'s life, but for all of Romana.