Introverted classical pianist and top student Kaoru Nishimi has just arrived in Kyushu for his first year of high school. Having constantly moved from place to place since his childhood, he abandons all hope of fitting in, preparing himself for another lonely, meaningless year. That is, until he encounters the notorious delinquent Sentarou Kawabuchi. Sentarou's immeasurable love for jazz music inspires Kaoru to learn more about the genre, and as a result, he slowly starts to break out of his shell, making his very first friend. Kaoru begins playing the piano at after-school jazz sessions, located in the basement of fellow student Ritsuko Mukae's family-owned record shop. As he discovers the immense joy of using his musical talents to bring enjoyment to himself and others, Kaoru's summer might just crescendo into one that he will remember forever. Sakamichi no Apollon is a heartwarming story of friendship, music, and love that follows three unique individuals brought together by their mutual appreciation for jazz.

One day, high school friends Akira Houjou and Chiaki Asami flip a coin and make a vow that completely changes their fates. For his part, Akira immediately drops out of school to join the yakuza, while Chiaki toughs it out in order to become a politician's aide. Although they seem to have made polar opposite choices, the two friends feel as if they are two sides of the same coin; they will do whatever it takes to reform Japanese society as they see fit.

Ten years ago, the Zol Empire conquered the neighboring lands of Aquafa, forcibly merging the two nations. Though the effort was a success, the Zol invasion could not seize Fire Horse Village, where an outbreak of a mysterious deadly disease known as Black Wolf Fever occurred. Since then, the people have believed the illness has been eradicated. At a salt mine overseen by Zol authorities, Van Gansa is a prisoner of war carrying out a forced labor sentence. One night, a pack of spirit-like wolves attack the mine; while Van and a young girl named Yuna are bitten, the two escape as the only survivors. In the official investigation following the incident, the findings indicate that the wolves were carriers of Black Wolf Fever, which led to the swift deaths of the guards and workers. Eager to experience freedom again, Van wastes no time settling down with Yuna in a small farming village. However, Van does not know that he is being followed. Pursued both by those who wish to harvest his blood to cure Black Wolf Fever and those who want to stop those efforts at all costs, Van faces a greater issue plaguing the nation that may spread to countries beyond.

In 1994, Kyousuke Kasuga is a war photographer covering the Bosnian War. However, in 1991, he was still an awkward college student struggling to be at ease in his relationship with Madoka Ayukawa. When Kyousuke is hit by a car in 1991, his soul becomes entangled with the soul of his future self. Struggling to understand the changes of the past three years, Kyousuke runs into Hikaru Hiyama, who has become a successful Broadway performer. As he tries to comprehend the feelings of the women in his life, Kyousuke must find a way to get back to the time where he belongs.