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.

Tsurune—It's the sound made by the bowstring when an arrow is released, and the sound that inspired Minato Narumiya to learn kyudo, a modern Japanese martial art focusing on archery. However, an incident during his last middle school tournament caused him to quit the sport. But soon, many factors conspire to make Minato take up the bow once again: the start of a new kyudo club in his high school, a chance encounter with a mysterious archer, and the support of his childhood friends, Seiya Takehaya and Ryouhei Yamanouchi. Together with his childhood friends and his new teammates, Kaito Onogi and Nanao Kisaragi, Minato rekindles his love for kyudo and works with his team toward their aim of winning the prefectural tournament.

After barely escaping a collision with a gigantic Gauna at the cost of many human lives, Kobayashi—the captain of the spaceship Sidonia—is prompted to change her political paradigm. Once she seizes full power, Kobayashi aims to eradicate the Gaunas from the Lem system where former Sidonians have recently established a colony. Her ambition is justified by two breakthroughs: the development of highly effective, long-range anti-Gauna weapons, and the creation of Tsumugi Shiraui—the first human-Gauna chimera possessing great destructive power. Facing hostility toward chimeras and her uncertain large-scale military expedition, Kobayashi enlists the help of the new elite pilot Nagate Tanikaze. Due to his personal experiences with Shizuka Hoshijiro and Benisuzume's placenta, Tanikaze soon develops a close bond with Tsumugi. As the final battle against humanity's most formidable opponent approaches, Tanikaze tries to enjoy the last days of peace with his friend Izana Shinatose—all while Kobayashi secretly pursues the development of an experimental weapon that could very well lead to the complete destruction of Sidonia.

A human may become a vampire only if they fall in love with one—and 14-year-old Kou Yamori wishes for nothing more. Kou has decided to fall in love with a vampire named Nazuna Nanakusa, and he has only 10 months of nightly rendezvous left to realize his goal. Kou's friends, Mahiru Seki and Akira Asai, are slowly coming to terms with the existence of vampires and Kou's decision to become one. As Kou realizes that a woman close to Mahiru is a vampire, he is unsure whether to support this relationship. Meanwhile, Anko Uguisu, the human detective bent on killing vampires, closes in on Nazuna and her coven. When an encounter leaves one of the vampires seriously injured, they learn that their human memories hold the key to a weakness that can be their demise—and to protect Nazuna, Kou must find out about her past.