Grisaia no Rakuen begins right at the end of the previous installment, Grisaia no Meikyuu. Kazami Yuuji is arrested under suspicion for terrorism. A video showing apparently concrete proof that Yuuji committed these acts, and he is held in custody by Ichigaya. Ichigaya knows full well that Yuuji didn't commit the crimes he has been accused of. But he did fail to assassinate Heath Oslo, who is the leader of the terrorist organization with an extremely devastating weapon in their possession. In fact, Ichigaya have their own plans for Yuuji... But all may not be lost for Yuuji. The girls of the Mihama Academy are not about to let Yuuji be used for political gain, and neither may the mysterious new figure which appears before them.

Aside from her deep passion for eating cakes, the clumsy Ichigo Amano has never been successful at anything. After an encounter with Henri Lucas, a famous patissier, Ichigo's amazing tasting abilities—although unbeknownst to her—are discovered. Recognizing her talent, Henri offers her the chance to attend St. Marie Academy, a prestigious culinary school which specializes in desserts. In spite of the fact that she is a beginner lacking skills, thanks to Henri's recommendation, Ichigo is placed in the topmost group with the "Sweets Princes." The princes, famous throughout the school for their magical treats, are Sennosuke Andou, an expert in traditional Japanese sweets; Satsuki Hanabusa, with a flair for candied flowers; and Makoto Kashino, a gifted chocolatier. Ichigo and the Sweets Princes, each accompanied by their "Sweets Spirits"—fairies who make patissiers' dreams come true—all work towards their goals in the competitive world of sweets.

Nozomu Itoshiki is still the bizarre teacher of the even stranger Class 2-F. He attempts to teach his students the negative aspects of the world and society, only to have each circumstance thrown at his face whenever he tries. With more students and friends than before, Zetsubo-sensei's life becomes harder and crazier than ever before. (Source: ANN)

Death City is home to the famous Death Weapon Meister Academy, a technical academy headed by the Shinigami—Lord Death himself. Its mission: to raise "Death Scythes" for the Shinigami to wield against the many evils of their fantastical world. These Death Scythes, however, are not made from physical weapons; rather, they are born from human hybrids who have the ability to transform their bodies into Demon Weapons, and only after they have consumed the souls of 99 evil beings and one witch's soul. Soul Eater Evans, a Demon Scythe who only seems to care about what's cool, aims to become a Death Scythe with the help of his straight-laced wielder, or meister, Maka Albarn. The contrasting duo work and study alongside the hot headed Black☆Star and his caring weapon Tsubaki, as well as the Shinigami's own son, Death the Kid, an obsessive-compulsive dual wielder of twin pistols Patty and Liz. Soul Eater follows these students of Shibusen as they take on missions to collect souls and protect the city from the world's threats while working together under the snickering sun to become sounder in mind, body, and soul. [Written by MAL Rewrite]