Kou Ichinomiya has always lived according to the creed of his wealthy, successful family: never be in debt to anyone. But one day, under the Arakawa Bridge, his life is saved by a homeless girl named Nino. In order to pay her back, Kou promises to be her boyfriend; and thus begins his new life under the bridge.

Through the introduction of his friend Danma Ryuji, Onizuka Eikichi, the former legendary bike gang member, visits Meishu Academy to tend to the trees in the garden as a part-time gardener. Learning that Yoshikawa Noboru, a student in teacher Fuyutsuki Azusa’s class is being bullied by Uehara Kyoko and other classmates, Onizuka befriends and saves Yoshikawa. Seeing Onizuka’s unprecedented but visceral, powerful response to problem solving, the school’s president and principal, Sakurai Yoshiko, overrides resistance from her vice principal Uchiyamada Hiroshi and makes Onizuka a teacher. Onizuka goes on to tackle many issues as the teacher in charge of the most problematic class, Class 2-4.

The cramped town of Keiko-cho is stained black with factory exhaust and oil. Late one night, a piercing whistle echoes from some ruins in a seemingly empty corner of the town, accompanied by the eerie echoes of harsh words spoken in German. The sounds come from a group of nine boys dressed in the starched collars and caps of high school uniforms. There in the darkness stands a secret base built by these nine boys under the leadership of Zera, the "king of the ruins," known as the Light Club.

A young boy, J. Shuro, meets the legendary pitcher Eiji Sawamura in the Philippines during World War II. Sawamura shares his dreams of one day gathering the nine Astro Superhumans – who all were born nine minutes and nine seconds past nine on September 9th of the 29th year of Showa (1954) and all have baseball-shaped birthmarks on their bodies – to form the ultimate baseball team capable of beating the Yomiuri Giants and any U.S. Major League team. When Sawamura dies during the war, Shuro decides to help fulfill his idol’s dream and goes in search of the nine ball players. But the team that is formed does not play ordinary ball. These extraordinary players demonstrate extraordinary plays on the field and some will not stop until everything – even their lives – is left on the field.