The game and anime follow Kon Hokaze, a boy who embarks on a journey from our world to an alternate world known as Mira, which is full a mysterious energy known as Alma. After saving Princess Ecarlate from attackers, he soon finds himself in the middle of a struggle around Alma.

In the kingdom of Earlshide, Merlin Walford was once regarded as a national hero, hailed for both his power and achievements. Preferring a quiet life however, he secludes himself deep in the rural woods, dedicating his time to raising an orphan that he saved. This orphan is Shin, a normal salaryman in modern-day Japan who was reincarnated into Merlin's world while still retaining his past memories. As the years pass, Shin displays unparalleled talent in both magic casting and martial arts, much to Merlin's constant amazement. On his 15th birthday however, it becomes apparent that Shin only developed his combat skills and nothing else, leaving him with blatant social awkwardness, a lack of common sense, and a middling sense of responsibility. As a result, Shin enrolls in the kingdom's Magic Academy to hone his skills and mature among other teenagers. However, living a normal life is impossible, as he is established as a local celebrity almost as soon as he arrives. Kenja no Mago follows Shin Walford's high school life in the capital as he makes new friends, learns about the world, and fights off the various forces of evil surrounding him and his city.

The day is as normal as it can be in high school as the students peacefully go about their everyday activities until an unprecedented catastrophe strikes the school, killing every person in its wake. Guided by what seems to be a miracle, a handful of students are fortunate enough to be reincarnated into another world as nobles, princes, and other kinds of people with prestigious backgrounds. One girl, however, is not so lucky. Being reborn as a spider of the weakest kind, she immediately experiences the hardships of her dire situation. Even so, she must press on to survive the numerous threats that endanger her life. Discovering that her new world has a system like that of an RPG, she tries her best to hunt prey and defeat monsters to level up and evolve. As she gradually grows stronger, she hopes one day her efforts will be rewarded, and that she will be granted a better life.

Although Kenzaburou Tondabayashi is a 52-year-old bureaucrat, he is well versed in reincarnation stories where a protagonist suddenly awakens in a fantasy world. After being hit by a truck, Kenzaburou lands in that exact situation. However, what baffles him is the fact he wound up in the world of an otome game—as the young villainess and the daughter of a duke, Grace Auvergne. Fortunately for Kenzaburou, he is somewhat familiar with his new world, as it is based on the game called Magical Academy: Love & Beast. He was a proud father in his previous life, and he often listened to his daughter rave about the game's setting and characters. Armed with background knowledge and a lifetime's worth of dad skills, Kenzaburou strives to make the most of his new life, though his kind-hearted nature makes it difficult to fully embrace the role of a villainess.