High school student Haruka has always been a content loner. One day, he and his class are abruptly transported to another world and given skill points to use when choosing from an assortment of abilities and magical powers. Unfortunately, Haruka arrives last, and he can only use his points on the seemingly impractical abilities the others had no interest in. Although he is on his own again and must adjust to his new life by himself, he much prefers it that way. However, Haruka's peaceful solitude is short-lived, as he runs into some of his classmates. Weak to their pleas for help, he ends up sheltering and helping them reunite with the others. But the different cliques struggle to see eye to eye, forcing Haruka to find a way to end the infighting and restore harmony between them to survive the unfamiliar world.

Hoping to unite their countries with an alliance, The Empress of Austria arranges her daughter, the delightful yet spoiled Marie Antoinette, to marry the crown prince of France, Louis XVI. Upon arriving in Versailles, the Austrian princess meets Oscar Francois de Jarjayes, Captain of the Royal Guards—a seemingly dashing young man—but to Antoinette's astonishment, he is in fact a woman! The youngest daughter of a noble family with a prominent lack of a male heir, Oscar was raised as a boy to continue the family's military legacy. Suffocated by the rigid rules associated with her new position and longing for companionship, Antoinette immediately takes a liking to this intriguing young woman, and wastes no time befriending her. However, as the childish new queen foolishly abuses her power, Oscar is conflicted between maintaining her loyalty to the royal family and addressing the growing concern of poverty among the common people. Recalling the events of the French Revolution, Versailles no Bara depicts the struggles of two women unjustly burdened by family expectations. Yet, despite being forced to deny their identities at the expense of personal happiness, they march on to become key players in the annals of history.

To commemorate the anime Flying Witch, the first volume of the Blu-ray/DVD release included a special episode of Flying Witch Petit.

Hanaoka high school is an all girls' school, and the girls were pretty excited when they heard that boys were admitted into their high school. Smart and elegant boys, that's in their fantasy. However, in reality, the boys who were actually admitted are from the countryside and not smart at all, leave alone being elegant. And in fact, two of them are dirty perverts...