Princess Anisphia "Anis" Wynn Palletia has always dreamed of flying through the sky, even though the people of her kingdom consider it a silly ambition. Also at odds with her goal is the fact that Anis is incapable of using magic despite her noble status. Refusing to give up so easily, she renounces her right to the throne, and focuses on developing "magicology" by combining various resources with knowledge from her previous life on Earth. Due to Anis' nature, responsibility for the kingdom's future is passed onto her younger brother, Algard. Pushed into a political marriage with Euphyllia Magenta, a girl he hardly knows, Algard rebels by spending more time with a commoner girl than his fiancée. After Euphyllia tries to intervene, Algard publicly calls off their marriage and denounces his ex-fiancée as a bully. After crashing into the banquet where Algard makes the announcement, Anis rescues Euphyllia on the flying broom she is testing. She decides to make Euphyllia her assistant, which the other girl reluctantly agrees to. Although their partnership appears random at first, Anis has an ulterior motive for wanting Euphyllia's company.

During the summer holidays, energetic Hana Uzaki spent most of her time accompanying her lonesome upperclassman, Shinichi Sakurai. Now that school has resumed, Uzaki's teasing continues to ramp up, much to Sakurai's constant annoyance. Nevertheless, no amount of ridicule can damage the pair's relationship—which only seems to be getting better as their college days fly by!

One day, Nobita picks a small rocket from which a small-sized humanoid alien named Papi comes out. He comes to Earth from a planet name Pirika to escape its evil PCIA army. At first, Doraemon and his friends are confused by Papi's small size, but with the gadget "Small Light", they shrink and play together. However, the whale-shaped battleship which was chasing Papi comes to Earth and attacks them. Papi blames himself for having involved everyone but, tries to fight against the PCIA army. In order to protect Papi and his planet, Doraemon and his friends travel to Pirika.

Ittoki Sakuraba fails to understand why his mother, his uncle, and his childhood friend, Kousetsu, seem to take his security so seriously. Kousetsu constantly follows and observes him with no regard for his privacy, focusing only on keeping him safe every waking moment. But the consistent hounding starts making sense when an adorable second-year student at his high school, Satomi Tsubaki, asks Ittoki out on a date. Though initially innocent, Tsubaki's true intentions soon become apparent when Ittoki visits her house; she plans to assassinate him, and she is not alone. Surprisingly, the ones who come to his aid are his uncle and Kousetsu—donning their dark and deadly ninja attire. After Ittoki is escorted to safety, his mother reveals the truth: he is the 19th heir to a noble clan of ninjas known as the Iga, and the target of assassination by their rival clan, the Koga. In order to protect himself against this new threat, Ittoki must hone his skills at the only ninja academy remaining in Japan: the Kokuten Ninja Academy.