The Shepherd, an urban legend of Shiomi Academy, is said to appear before hardworking students to grant them a wish. While engrossed in a book inside the school's renowned Great Library, Kyoutarou Kakei, a second year student and the Library Club's de facto president, receives an email from the Shepherd foretelling an event that will change his fate. Worried by the message, Kyoutarou rushes over to a nearby train station and encounters fellow student Tsugumi Shirasaki, whom he saves from being hit by a derailing train. Grateful for his heroic actions, Tsugumi joins the Library Club and invites Kyoutarou to participate in her mysterious Shiomi Happy Project. Together with other new members of the club, they strive to make the academy a better place and uncover the identity of the enigmatic Shepherd.

Rumor has it that if a young girl strikes a bargain with a white fairy, it will grant any wish her heart desires. However, in exchange, she will become a magical girl and must put her life on the line to slay fearsome and ferocious witches. Iroha Tamaki, a kind-hearted middle schooler from Takarazaki City, is living proof that these rumors are true. Armed with a magical crossbow and the ability to heal injuries, Iroha seeks out the labyrinths where witches hide and defeats them before they can prey on humans. Yet Iroha has no memory of her wish, and even Kyuubey, the white fairy himself, seems to have no idea what Iroha requested of him. One day, Iroha hears rumors of a city where magical girls can be saved, and finds herself on a sunset train to Kamihama City. Unfortunately, she discovers that the witches in Kamihama are far more powerful than usual. After veteran magical girl Yachiyo Nanami is forced to save her, Iroha vows to never return. But when a chance encounter with a tiny Kyuubey seems to trigger distant memories, Iroha is compelled to investigate the mysterious city despite the danger.

Like the R Season, Sailor Stars is divided into two parts: The first part resolves some conflicts from the SuperS season, and sees the return of the Outer Senshi, Haruka, Michiru, Setsuna, and Hotaru (now reborn as a child). In the second part Usagi bids farewell to Mamoru, who is going to America to study. At the same time, the Three Lights apper, an idol trio consisting of three boys, Seiya, Taiki, and Yaten. The new enemy is Galaxia, a woman who desires to rule the entire galaxy by collecting the Star Seeds of humans. Three new Senshi appear, the Sailor Starlights, who have their own reasons to stop Galaxia, but without Sailor Moon's help.

Six months ago, Lord Hugh Anthony Disward, also known as Huey, lost his eccentric grandfather, Sir Wesley Disward, who was a renowned collector of rare books. His grandfather's will states that, in order to inherit his manor and everything inside it, he must take guardianship over the Bibliotheca Mystica de Dantalian—an archive that contains forbidden knowledge—and also take care of a mysterious girl called Dalian. As Huey settles into the manor, an old rival of his grandfather's arranges a meeting with him. Dalian, knowing the rival to be Wesley's killer, tags along and discovers that the murderer is in possession of a Phantom Book—a cursed tome that Wesley tried to seal away. When the book puts the two in danger, Huey discovers that the Bibliotheca Mystica de Dantalian and Dalian are one and the same, and she entrusts Huey with the key to unlocking the knowledge stored within her. Together, Dalian and Huey seal the book away, and thus begins an unlikely partnership as they solve mysteries caused by other Phantom Books.