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.

Yuuta Segawa has just started his freshman year of university. One day, his sister Yuri, who raised him after their parents died, asks him to take care of her daughters Hina, Sora and Miu while she and her husband go overseas on a business trip. Yuuta grudgingly accepts, but tragedy strikes when their plane goes missing and all passengers are presumed dead. In an effort to prevent the three girls from being split up, Yuuta goes against their family and takes them in, just as his sister took him in when he had no one else. Now the four find themselves in a new and peculiar situation: Yuuta must learn how to balance his new responsibilities—as the newest member of the Street Observation Research Society, a club for people watching, and also as a father figure—while Sora, Miu, and Hina come to terms with the loss of their parents.

Love is unusual for Risa Koizumi and Atsushi Ootani, who are both striving to find their ideal partner in high school—172 cm tall Koizumi is much taller than the average girl, and Ootani is much shorter than the average guy at 156 cm. To add to their plights, their crushes fall in love with each other, leaving Koizumi and Ootani comically flustered and heartbroken. To make matters worse, they're even labeled as a comedy duo by their homeroom teacher due to their personalities and the stark difference in their heights, and their classmates even think of their arguments as sketches. Lovely★Complex follows Koizumi and Ootani as they encourage each other in finding love and become close friends. Apart from their ridiculous antics, they soon find out an unexpected similarity in their music and fashion tastes. Maybe they possess a chemistry yet unknown, but could love ever bloom between the mismatched pair?

Yako Katsuragi is an acclaimed high school detective, who, despite her young age, has solved many cases. In fact, there seems to be no case that she cannot solve, or any culprit that escapes justice. But within the walls of her detective agency lies the secret to her prolific crime-solving skills: the cases are actually solved by her assistant, Neuro Nougami. However, to call Neuro an ordinary man would be incorrect. In reality, he is a demon, who came to the human world in search of the ultimate mystery, having already solved every mystery in the demon world. With Yako as his proxy, he feasts on the negative energy released by humans when they commit crimes. Thus, he promises to help Yako solve the mystery of her father's death. But to do so, he must avoid drawing too much attention to himself, which is why Yako plays the role of the detective. As Yako desperately searches for the truth of her father's death, the unlikely duo continues to solve case after case in order to satisfy Neuro's ravenous appetite.