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.

In her everyday life, Yuuna Yuuki is a hero. As proof, she is in her middle school's Hero Club, where she does her best to help others and bring a smile to everyone's face. But Yuuna, always up to any task, is about to become an even bigger hero. Mysterious destructive forces called Vertexes begin threatening the world she loves, and the Hero Club is called upon by a strange phone app to save it. Along with her best friend Mimori Tougou, as well as sisters Fuu and Itsuki Inubouzaki, they must transform into magical girls in order to battle the Vertexes. In between studying and putting on shows for kids, Yuuna and the Hero Club must fight for the very existence of their world and face the harsh truths behind their own powers, all the while discovering what it truly means to be a hero.

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.

In a distant future, Earth has become a wasteland and humanity as we know it has died out. All that remains are sentient robots. They were supposed to be able to live forever—until the one called Luna died and the Ruin started. Their bodies will rust, and there is nothing that can be done to fix it. Now the robots are left only to contemplate their deaths, kept going only by the rumor that if they eat the one called Casshern, they will gain immortality. Casshern knows nothing about his past, why he exists, or what he is, but he must find out, or he will face the constant torment of being hunted by robots who don't want to die. Casshern leaves death wherever he goes, but he must face it if he is to find out the truth of this world.