Since the demise of the man believed to be Britannia's most wicked emperor one year ago, the world has enjoyed an unprecedented peace under the guidance of the United Federation of Nations. However, this fragile calm is shattered when armed militants successfully kidnap former princess Nunnally vi Britannia and Suzaku Kururugi, the chief advisor of the Black Knights, sparking an international crisis.

The powerful and untrustworthy Kingdom of Zilkhstan is accused of orchestrating their capture. To investigate, world authorities send Kallen Stadtfeld and her associates on a covert operation into the country. There, they encounter the immortal witch C.C., who is on a mission to complete the resurrection of the man responsible for the greatest revolution in history—a legend who will rise up, take command, and save the world from peril once again.

Two years ago, a mysterious wind swept over the Earth without warning, taking everyone's memories with it. Not knowing their names or even how to speak, cars crashed, planes dropped from the sky, and society crumbled in an instant. One young man happens to wander into a military testing facility, where he meets Johnny, a young boy who underwent experimental memory enhancement treatment and could, therefore, still remember who he was. Johnny names the young man Wataru and teaches him everything that he can before his frail body fails him. Wataru sets out on a journey to see if he can find other people like him, and in San Francisco, he meets a mysterious silver-haired woman named Sophia, who refuses to speak about her past. Sophia says that she is heading to New York, and decides to travel together with Wataru. As the pair make their way across America, they learn about what has happened to the rest of society, and what the essence of humanity really is.

On the planet Amoi, a person's status is primarily dictated by the color of their hair. This society is run by the AI supercomputer known as Jupiter and its governing board of perfect blondes, referred to as Blondies, living in the capital city of Tanagura. However, the darker-haired humans live out their lives in the golden "pleasure city" of Midas and its outlying slum Ceres. They are known as "mongrels," and most cannot progress out of the slums. Three years ago, a boy named Riki disappeared from the slums of Ceres. Once the revered leader of the gang Bison, a sudden encounter with an elite Blondie, Iason Mink, forced Riki to abandon everything he had cultivated. The boy was snatched from his home and forced to become Iason's pet. Riki has spent the past three years enduring numerous blows to his pride, his time in Tanagura nothing but a form of torture. Now that Riki has returned, Bison once again rallies behind him. The risk he finds himself in, however, is much greater than ever before—there is always someone ready to sell him out.

While Randy was walking through the Swiss countryside he finds a small girl, who seemed to be the only survived person from an airplane crash. The little girl didn’t remember anything, and Randy decided to take care of her and he called her Judy. The both go their childhood together. A few years later, Judy, now 16 years old, wants to find her past. With the help of Randy, she leaves to research her origins. Her single clue is a song that she keeps hearing in her head, the song is called Alpine Rose. At a time of world war, these two young people will have to overcome many obstacles to arrive at their goal in this time of war, with having only each other to comfort and support. the depth of their love.