Because of the constantly declining birth rates over many decades, human civilization is all but extinct. With only a few humans remaining, they survive in this post-apocalyptic world with what was left behind by the previous generations. Earth is now dominated by fairies, tiny creatures with extremely advanced technology, an obsession with candy, and a complete disregard for human safety. A young girl who has just finished her studies returns to her hometown and is designated as an official United Nations arbitrator. Her duty is to serve as a link between mankind and fairies, reassuring each side that both races can live together peacefully. She imagines this task will be easy enough, but controlling the disasters created by the oblivious fairies in their pursuit of candy will require a lot more effort than she initially believes.

At the stroke of midnight, the Dark Hour appears—a secret hour which most are unaware of. Those not trapped in coffins during this time, unfortunate enough to find themselves conscious, are met by dangerous creatures known as Shadows. A select few, however, possess the potential to wield Persona: a special power used to defeat these beings. This secret group is called SEES (Specialized Extracurricular Execution Squad), and their mission is to uncover the reason behind the Dark Hour's appearance. Only a short while after transfer student Makoto Yuuki begins his residency at Iwatodai Dorm, his Persona awakens after an attack by a strong Shadow. Now recruited into the ranks of SEES, he begins fighting alongside his comrades, as only they can protect humanity from Shadows and prevent the anomaly that is the Dark Hour.

Van, a lanky and apathetic swordsman, is on a journey to kill the murderer of his fiancé. The only characteristic he has to go by is that the murderer has a claw for an arm, hence the murderer being referred to as The Claw Man. During his travels, Van happens to pass through the city of Evergreen, which is defending itself from bandits who aim to rob the city of its treasury. It is in this city that Van meets Wendy Garret, a timid young girl who is looking for her kidnapped brother. When the city pleads for Van's assistance to defend it, he refuses, claiming it has nothing to do with him and thus leaves the city on its own to deal with the peril. Soon after, Van comes across the raiding bandits himself and they eventually tick off the swordsman to a degree where he takes action against them for his own personal vendetta. Surprisingly, Van learns that the bandits had ties with The Claw Man, and in kidnapping Wendy's brother for a reason they did not disclose. After the bandits are dealt with easily, Van and, much to his chagrin, Wendy continue the journey in search of The Claw Man. Little do they know, however, that The Claw Man is involved with something more atrocious than either could fathom.

Ever since he was a child, Tomoki Sakurai has always woke up with tears after a dream of an angel. His childhood friend Sohara Mitsuki worries about this and decides to seek the help of Eishirou Sugata, an eccentric sky maniac. He concludes that Tomoki's dream is undoubtedly connected to what is known as the New World, a floating anomaly that scientists have failed to understand. Recruiting the New World Discovery Club's first members, Eishirou schedules a time to meet up in order to observe the mystery in the sky. That day, Tomoki's peaceful life is changed forever when a strange girl falls from the sky and begins to call him master. Sora no Otoshimono follows the daily activities of the New World Discovery Club as they begin to learn more about the Angeloids that have arrived on Earth.