In humanity's distant future, two interstellar states - the monarchic Galactic Empire and the democratic Free Planets Alliance - are embroiled in a never-ending war. The story focuses on the exploits of rivals Reinhard von Müsel and Yang Wen Li as they rise to power and fame in the Galactic Empire and the Free Planets Alliance.

Shortly after the Inter-High of Kagami and Kuroko's second-year, a street basketball team from the USA called Team Jabberwock came to Japan to play a friendly match against a Japanese college-level street basketball team, Team Strky. Despite their best efforts, Strky is brutally crushed by Jabberwock. After the match, the Jabberwock players insult the players from Strky and all of Japanese basketball, claiming Strky's basketball was at the same level as monkeys and telling the players and crowds to quit playing basketball and kill themselves. As a revenge match, Kagetora assembles a dream team of all members of Generation of Miracles plus Kuroko Tetsuya and Kagami Taiga, along with bench players Hyūga Junpei, Takao Kazunari, and Wakamatsu Kōsuke, forming Team Vorpal Swords, with the hopes of reclaiming the pride of Japanese basketball.

The year is 1863 as the tumultuous samurai era is coming to an end, Japan is split between the pro-shogunate and anti-shogunate factions. The fate of the world is threatened as an army of historical revisionists are sent from the future to alter the course of history. In order to bring these forces down and protect the real history, two sword warriors, spirits who are swords brought to life by Saniwa (sage), rush to Edo. The polite and thoughtful Horikawa Kunihiro and the short tempered yet skillful Izuminokami Kanesada, who served the same master, confront the invading army along with a lively gang of other warriors including Mutsunokami Yoshiyuki, Yagen Toushirou, Tombokiri, and Tsurumaru Kuninaga. As the fate of history lies in these hero's hands, what meets the blade is yet to be uncovered...

A floating space without gravity where an infinite number of lights shine in different colors: The "Box of Wisdom." Inside of this box, there are multiple worlds, multiple timelines, and there used to be many different people. This is where Dual and Dorothy were fighting with enemies called "Viruses." Worlds infected by viruses must be erased. That is the duty, the job of these girls. However, one day, Dual and Dorothy feel the presence of a new Virus. Arriving at the scene, they see a girl being attacked by Viruses. After saving the girl, the duo wait for her to awaken so they can ask who she is, where she came from, and where she is going. Finally, when the girl opened her eyes, she gave her name, Rimo, and whispered only one sentence... "I must return to the flower patch..."

Yuugo Hachiken enrolled in Ooezo Agricultural High School for the reason that he could live in a dorm there. In some ways he chose Ooezo in an effort to escape the highly competitive prep schools he had attended previously, but he was faced with an entirely new set of difficulties at Oezo, surrounded by animals and Mother Nature. After growing up in an average family, he began to encounter clubs and training the likes of which he had never seen before.

Ishida & Asakura focuses on the title characters—the stoic Ishida and the lecherous Asakura—and the bizarre students and teachers that populate their high school. Asakura is obsessed with curvaceous women and dreams of becoming a teacher in order to be surrounded by attractive girls all day. Ishida dreams of running a flower shop together with Asakura after they finish high school, and appears to have strong homosexual feelings for his best friend, although this is always played for laughs.