Slam Dunk centers around Hanamichi Sakuragi, who starts as a delinquent outcast, becoming the leader of a gang. Hanamichi, being very unpopular with girls, has been rejected by them fifty times. Yet, he finds out that Haruko Akagi is the girl of his dreams, and is happy when she's not scared of him like all the other girls he has asked out. Haruko Akagi, who recognizes Hanamichi's athleticism, introduces him to the Shohoku basketball team. Hanamichi was reluctant to join the team at first because he had no previous background in any sports and thought that basketball was a game for losers (also because the fiftieth girl rejected him for a basketball player). Sakuragi, despite his immaturity and hot temper, proves to be a natural athlete with potential and joins the team in order to impress Haruko and prove that he is worthy of her. Later on, Sakuragi realizes that his love for the sport equals that of his crush on Haruko. Kaede Rukawa — Sakuragi's bitter rival (both on the basketball court and love, even when Rukawa doesn't acknowledge Haruko's crush on him), the star rookie and a "girl magnet" - joins the team at the same time. Hisashi Mitsui, an ex-junior high school MVP, and Ryota Miyagi, a short but fast player, both also rejoin the team and together these four struggle to complete team captain Takenori Akagi's dream of making Shohoku the national champion. Together, these misfits gain publicity and the once little known Shohoku basketball team becomes an all-star contender in Japan.
Middle-school student Miaka Yūki feels a lot of pressure to pass the entrance exam for the competitive Jonan Academy. Her friends do not believe she will get in, but she is determined to because her mom expects her to. Her best friend, Yui Hongo, is smart and has also applied to the Jonan Academy. While at the library one day, Miaka and Yui encounter a strange book known as The Universe of the Four Gods. Reading this book transports them into the novel's universe. However, Yui is transported back to the real world almost immediately. Inside the novel, Miaka finds herself the Priestess of Suzaku, destined to gather the seven Celestial Warriors of the god Suzaku in order to summon Suzaku and obtain three wishes. She falls in love with the Celestial Warrior Tamahome, who eventually reciprocates and Miaka's desire to use a wish to enter the high school of her choice begins to shift towards finding a way to be with Tamahome. Yui, who is also drawn into the book when she was trying to help Miaka to come back to the real world, becomes the Priestess of Seiryuu, working against Miaka out of jealousy over Tamahome and revenge for the humiliation and pain she had suffered when she first came to the book world.
The series describes the various trials that teenagers Miaka and Yui face, both quest-driven and personal. Feeling betrayed, the two oppose one another as priestesses, bringing together their own respective warriors and vying for the chance to be granted one wish by the gods whom they hope to summon.
Twelve years prior to the start of the story, Ging Freecss left his infant son, Gon Freecss, with Gon's aunt, Mito Freecss, on Whale Island. Gon, who was told all his life that both his parents were dead, finds out from Ging's apprentice, Kite, that his father is still alive and has since become an accomplished Hunter. Hunters are licensed, elite members of humanity who are capable of tracking down secret treasures, rare beasts, or even other individuals. Gon leaves his home to become a Hunter like his father by taking the Hunter Exam, a series of brutal tests involving skill, survival, and teamwork. Prior to and during the exam, Gon meets and befriends three of the other applicants: the last remaining member of the Kurta clan, Kurapika, who wishes to become a Hunter in order to avenge his slain people; Leorio Paladinight, a prospective physician who claims to desire to become rich; and Killua Zoldyck, who had left his life as a member of a notorious assassin family. Among many other examinees, Gon continuously encounters Hisoka, a deadly, sadistic magician.