After accepting a weekend invitation, Hachiman Hikigaya accompanies Isshiki Iroha around the Chiba Prefecture to brainstorm ideas suitable for an ideal date with Hayato Hayama. As the duo wanders from place to place without a plan, they seemingly enjoy each other's company. Yet, through these straightforward and sincere interactions, the meaning behind what it means to be genuine continues to intrigue Hachiman and his outlook for the future of the Volunteer Service Club and its members.

Kimihiro Watanuki can see spirits and other assorted supernatural creatures, which is quite a bothersome ability he strongly dislikes. On the way home one day, while plagued by some spirits, he is inexplicably compelled to enter a strange house. There, he encounters Yuuko, a mysterious woman who claims to be able to rid him of the ability to see and attract the troublesome creatures—for a price. She demands that he work at her store that grants wishes to people, and thus begins Watanuki's adventures through weird and wonderful events.

Her name is Esumi Fuuka. Standing tall at 163 cm with a slender bodyline, she must be a university undergraduate; however, in reality, she is only an elementary school student. With a body figure of an adult and the mentality of a small child, she creates many misunderstandings around her.

In the 1960s, a gifted young medical student tries to make a name for himself. Kuroo Hazama is a reserved young man with unusual black-and-white hair, a body covered with scars, and a dark past. Despite only being a medical student, his surgical brilliance starts to attract attention after he completes a seemingly impossible operation. Together with the spirited and honest intern Maiko Okamoto and Yabu, a close friend with a troubled life, Hazama devotes himself to the world of medicine. However, his path to becoming a respectable surgeon is a difficult one as student riots, war, and corruption are consuming Japan. Hazama quickly finds himself caught up in a series of nefarious circumstances that challenge his integrity as a person and his path towards becoming a surgeon. Young Black Jack chronicles the story of a man capable of performing unthinkable feats of medicine, and the journey that leads him to become the legend known as Black Jack.