Teikou Middle School is famous for its highly renowned basketball team, which produced the famed "Generation of Miracles": a team of five prodigies, each with their own unique abilities, considered to be undefeatable by the time they became third years. However, blinded by pride, they split up, entering different high schools upon graduation.

Taiga Kagami, having just returned from America, joins the basketball team at Seirin High School in search of strong team members. There, he finds Tetsuya Kuroko, a seemingly unimpressive player, only for Kagami to find out that Kuroko was the "Phantom Sixth Member" of the Generation of Miracles: an invisible player who used his impeccable passing skills to support the team from the shadows. Together, they resolve to defeat the Generation of Miracles and make the Seirin basketball team the best in Japan.