Hailing from America, Jabberwock—a street basketball team with skills comparable to those of the NBA—has come to Japan to play an exhibition match against Strky, a team of former third-year students who once played in the Interhigh and Winter Cup. However, due to the vast difference in skill, Jabberwock easily wins. Their captain, Nash Gold Jr., mocks the basketball style of all players in Japan by comparing them to monkeys. Infuriated by the nasty comment, Kagetora Aida challenges them to a revenge match. Because of pride and the belief that the results will be no different, Nash accepts the challenge. Kagetora then assembles Vorpal Swords, a team composed of the Generation of Miracles, including Kuroko Tetsuya and Kagami Taiga, for they are the only ones who stand a chance against a foe that seems unbeatable from every angle.

For the last three years, Teikou Middle School has dominated the national basketball scene with its legendary lineup: the Generation of Miracles. It consisted of five prodigies who excelled at the sport, but a Phantom Sixth Man lurked in the shadows and helped earn the team their revered status. Eventually, their monstrous growth jaded them from the sport they loved and made them go their separate ways in high school. In search of new members, the Seirin High School basketball team recruits Taiga Kagami and Tetsuya Kuroko, two freshmen who seem to have significant differences in abilities. Having returned recently from America, Kagami has both a natural aptitude and relentless love for the sport. Meanwhile, Kuroko lacks presence and exhibits no outstanding athletic talent. However, it is later revealed that he is Teikou's Phantom Sixth Man—the player once part of the Generation of Miracles. Kuroko wants to prove to the Seirin team that he is strong in his own way. Seeing his conviction, Kagami forms a dynamic partnership with Kuroko, the latter promising to support Kagami's light as his shadow. Alongside their new Seirin teammates, they aim to conquer the upcoming Interhigh championship, but the reappearance of Kuroko's former teammates complicates their plan.

Seirin prepares to face major obstacles on their path to winning the Winter Cup, including the teams each possessing a member of the Generation of Miracles. Kuroko goes head-to-head with his old teammates once more as he attempts to show them that individual skill is not the only way to play basketball. His firm belief that his form of basketball, team play, is the right way to play the sport will clash with the talents of a perfect copy and an absolute authority. While Kuroko tries to prove that his basketball is right, he and the rest of Seirin High ultimately have one goal: to win the Winter Cup and overcome the strength of the Generation of Miracles, who have long dominated the scene of middle and high school basketball.

In 12th-century Japan, swordsman Kurou escapes ghastly pursuers into a deep forest with his servant Benkei. Seeking shelter, the two find themselves within the secluded abode of the mysterious and beautiful Kuromitsu. While they are warmly accepted, the men are warned to never enter Kuromitsu's room. However, driven by innate curiosity and perhaps a condemned love, Kurou peeks through the ajar door, only to find Kuromitsu feasting on the blood of fallen men. He soon learns Kuromitsu is an immortal vampire, and dedicates himself to her—even becoming a vampire himself in order to spend eternity with her. But the cryptic organization known as the Red Army has enlisted the help of Benkei, who betrays Kurou and severs his head. Awaking centuries into the future in an apocalyptic modern-day Japan, Kurou sets off to reunite with his lover and exact revenge on the Red Army.