Ikebukuro is home to many different businesses and gangs. This includes Makoto Majima: the infamous troubleshooter who mediates between warring factions. Makoto knows all of the ins and outs of the bustling Tokyo district and strives to maintain peace alongside the G-Boys, who assist Makoto in his troubleshooting endeavors. Led by the charismatic and ruthless Takashi Andou, the G-Boys is the most influential gang in all of Ikebukuro. However, when the new faction Red Angels begins to move in on the G-Boys' turf, immediate tensions rise between them. With numerous enemies scattered around and within the G-Boys, navigating through the streets becomes more difficult for Makoto. While continuing to troubleshoot problems, he slowly unravels a plot that may trigger an all-out war and threaten the entirety of Ikebukuro.

Despite endless research, the human mind remains a mystery to this day. Unknown to the public, there exist special individuals who are able to dive deep into the minds of people and even manipulate their memories. Gifted with this ability, Hiroki, Tsukasa, and Satoru are among those who use their power to commit crime under the orders of their leader, Katsuragi. The three step into the dangerous territory of the human mind in order to destroy their assigned targets while striving to keep their own minds and memories safe.

Joe Yabuki is a troubled youth, whose only solution to problems is throwing punches at them. What he lacks in manners and discipline, he makes up for with his self-taught fighting skills. One day, while wandering the slums of Doya, Joe gets into a fight with the local gang. Although greatly outnumbered, he effortlessly defeats them, drawing the attention of Danpei Tange—a former boxing coach turned alcoholic. Seeing his potential, he offers to train Joe into Japan's greatest boxer. At first, Joe dismisses Danpei as a hopeless drunk; but after the trainer saves his life, he agrees to live with him and learn the art of boxing. Unfortunately, Joe's personality makes him an unruly student, and he often falls back to his old ways. To survive the harsh world of his new career, Joe needs to trust his mentor and master the techniques taught to him. However, the road to becoming a professional boxer is rife with struggles that will test his mettle to the end.

Kivotos is a federal megalopolis comprising thousands of schools and is led by the General Student Council (GSC), which acts as its governing body. Ironically, despite being an academy city, Kivotos is rife with gun violence, and all students wield firearms as part of their everyday lives. As if the crisis in Kivotos was not enough, the GSC president is nowhere to be found. Fortunately, before her sudden disappearance, the GSC president enlisted the help of Sensei—a teacher who is most likely the only one in Kivotos—to support students in their time of need. Sensei's first course of action is to assist Abydos High School, a once prestigious academy now with merely five students in attendance. These remaining students are doing everything they can to pay their academy's crippling debt of almost one billion yen.