The film's story is set four years after the events of the original Shirobako anime. Aoi Miyamori keeps busy dealing with the ordinary troubles in her daily work at Musashino Animation. After a morning meeting, Watanabe talks to Aoi and puts her in charge of a new theatrical anime project for the studio. The project has unexpected problems, and Aoi is unsure if the company can proceed with a theatrical anime with its current state of affairs. While dealing with that anxiety, Aoi meets a new colleague named Kaede Miyai (voiced by Ayane Sakura). She and the MusAni team work together to complete the project.

Traumatized by school, Jun Sakurada spends his days at home as a shut-in, purchasing things online, only to send them back before the free trial period ends. So when a note appears on his desk, asking whether or not he would wind something, he assumes it was something he ordered and carelessly circles "yes," changing his life forever. A box arrives with a wind up doll inside, but this is no ordinary toy: after Jun winds her up, she begins walking and talking as if a normal person. With a haughty attitude, she introduces herself as Shinku, the fifth doll in the Rozen Maiden collection, a group of special dolls made by the legendary dollmaker Rozen. These sisters must battle each other in a competition called the Alice Game with the help of a human to ensure victory. The winner becomes Alice, a real girl who is worthy of meeting their creator. As more sentient dolls end up taking residence in Jun's house, and a foe from Shinku's past makes her appearance, Jun's life becomes far more complicated than he ever thought possible. [Written by MAL Rewrite]

The true end arc of Ore no Imouto. These four episodes branch out after the 11th episode of the main TV series and present an alternative version to the end of the TV series. These episodes contrast with the good end arc of the TV series, which was an original ending written for the anime, and instead closely follows the original story from the light novels.

Twenty-six-year-old Hiroto Suwa; his wife, Naho; and their old high school classmates—Takako Chino, Azusa Murasaka, and Saku Hagita—visit Mt. Koubou to view the cherry blossoms together. While watching the setting sun, they reminisce about Kakeru Naruse, their friend who died 10 years ago. Mourning for him, they decide to visit Kakeru's old home, where they learn the secret of his death from his grandmother. Filled with regret, Suwa and his friends decide to write letters to their 16-year-old past selves to set their hearts at rest. With the knowledge contained in the letter from his future self, 16-year-old Suwa has the chance to rewrite the future. What choices will he make? What will happen in this new future? [Written by MAL Rewrite]