Six years following the events of Chaos:Head, a new string of deaths similar to the New-Gen murders have started up in the newly rebuilt Shibuya area. These incidents have taken the attention of a Highschooler: Takuru Miyashiro, and the newspaper club. Investigating the incidents of the present as well as their connection to the events of the New-Gen Crimes Takuru and his friends find themselves being pulled deeper into the incidents than they ever believed possible.
The Empire of Britannia has invaded Japan using giant robot weapons called Knightmare Frames. Japan is now referred to as Area 11, and its people the 11's. A Britannian who was living in Japan at the time, Lelouch, vowed to his Japanese friend Suzaku that he'd destroy Britannia. Years later, Lelouch is in high school, but regularly skips out of school to go play chess and gamble on himself. One day, he stumbles on terrorists 11's who've stolen a military secret and is caught by a member of the Britannian task force sent after them, who is Suzaku. As the rest of the squad arrives, Suzaku is shot for disobeying orders, while the military secret, a young girl, gives Lelouch the power of Geass, which makes anyone obey any order. While Suzaku is secretly made the pilot of Britannia's brand new prototype Knightmare, Lancelot, Lelouch becomes the masked Zero to lead the rebellion to destroy Britannia once and for all.
Yuichi Aizawa returns to this city after seven years. In his childhood, he often visited it, but something happend in the past which caused him to block out his memories of the events of seven years ago. On the day after he gets settled in, he meets a girl carrying a backpack with wings on it. Her name is Tsukimiya Ayu and he begins to recall the memories he had lost.
Junpei Kōsaka is a second-year high school student who despises cats and has an allergy to them. It just so happens that his high school crush is Kaede Mizuno, a girl who adores cats. One day, while walking home from school, Junpei kicks an empty can and unfortunately beans the local neko-jizō-sama (guardian deity of cats). Soon, he finds he can now understand what cats are saying, including his family's own ill-tempered cat, Nyamusasu. However, if he does not grant 100 wishes from cats, he will turn into a cat himself.
High school sophomore Yuki Hase noticed that Kaori Fujimiya, his classmate, was always alone. He tried to start a conversation with her but was turned down: "My memories of friendship can last only a week," she said. Despite of knowing this shocking truth, Yuki keeps trying to be Kaori's "new" friend every week.