Fully believing in the legend of the thumb-sized princess, Shunichi and Chiyomi await the sunrise at Cape Akebono—but nothing happens. Feeling disheartened, and wanting to spare Shunichi any more hardship, Chiyomi breaks up with him. Overwhelmed with shock, Shunichi ends up getting hit by a car that comes speeding out of nowhere. Noriko, who had secretly been following Shunichi, discovers the shrunken Chiyomi, and together they rush to the hospital. But how is it all going to end?
High-school seniors Chiyomi and Shunichi were once childhood sweethearts, but have since drifted apart and have not spoken for several years. Chiyomi is initially pleased when her friend, Riku, confesses his feelings for her, but her joy is soon tempered by a chance sighting of Shunichi acting intimately with classmate Sayori. Suddenly, Chiyomi is forced to realize that she has never completely gotten over Shunichi. The stage is set for an eventful evening, during which a confused Chiyomi argues with her parents before bursting out of the house.
Caught in a rainstorm, Chiyomi reminisces about how much happier she was when she was a child and expresses a wish “to be little again.” Unfortunately, her wish is granted all too literally: She is transformed into a 16-centimeter version of herself! It is not until the following day that Shunichi discovers her in a park—and starts pinching himself in disbelief! Although her disappearance causes her family to fret, Chiyomi feels unable to return home in her present state, and instead begs a bewildered Shunichi to harbor her in his room.
Chiyomi decides to lie to her parents and pretend that she is attending a dance workshop in Tokyo. In the meantime, Shunichi sneaks Chiyomi into a local shrine that is home to a sacred mallet. According to a legend that Shunichi’s grandmother once told him, a thumb-sized princess attained human height with the help of this mallet. Shunichi hopes the mallet will have the same effect on Chiyomi, but ends up disappointed. His woes are compounded when he catches a cold and spends the following day in bed. When Sayori visits him unannounced to see how he is doing, she finds him asleep—and decides to use this opportunity to plant a kiss on him!
Shunichi initially rejects a plea from his friend Sho to rejoin the kendo team for an important match, but changes his mind after being encouraged by Chiyomi and his mother, Emiko. Although his team enters the match as underdogs, Shunichi puts up a good fight. In the end, however, he is defeated. As Shunichi wallows in self-pity behind the gym, Chiyomi finds herself unable to find the words to comfort him. Meanwhile, a suspicious man begins spying on Shunichi’s household.
Dissatisfied with Shunichi’s efforts to make miniature clothes from a handkerchief, Chiyomi daringly decides to head home and sneak out some outfits that she used to dress her dolls with when she was younger. After pulling this off undetected, she returns to Shunichi’s home—and is startled to find a mysterious couple there! Believing the man and woman to be burglars, she tries desperately to drive them away, and eventually succeeds by playing a CD at deafening volume. But her epic adventure is far from over!
While secretly attending school in the pocket of Shunichi’s uniform, Chiyomi happens to catch Riku’s eye. In a sudden rush of panic, she quickly ducks down out of sight. Meanwhile, on a visit to see her father in the hospital, Sayori is shocked to learn of his plans to remarry. Emiko witnesses all of this, and walks back from the hospital with Sayori, which leads to her staying over in the Minami household. That night, Sayori goes into Shunichi’s room, desperate for a kiss.
Shunichi’s grandmother, Tomiko, finds out about Chiyomi! The two then strike up a conversation, and it soon becomes clear that Tomiko is convinced Chiyomi is the thumb-sized princess of legend. That’s when Chiyomi’s mother, Noriko, comes over a visit; she has been worried about Tomiko’s strange recent behavior. Chiyomi overhears her mother complaining that Chiyomi’s father, Yuji, never actually proposed to her before they got married. And so, Chiyomi begins to think up a plan to get her father to propose to her mother after 18 years of marriage.
Tomiko is rushed to the hospital after a sudden fainting spell. The doctors detect nothing out of the ordinary, and admit Tomiko for observation. Shunichi is relieved to hear that Tomiko is no longer in any immediate danger, but after taking his eyes off of Chiyomi for one brief moment, he discovers that she’s been snatched away by one of the inpatients, a girl named Miyu. When Chiyomi learns Miyu is afraid that her mother, Miho, hates her, she tries to think of a way to get Miho’s true feelings across to Miyu. Meanwhile, Sayori asks Shunichi to step out into the hall with her for something important.
Suspicious that the main character in Chiyomi’s online novel, “Pocket-Sized Chobiko,” is in love with a character based on Shunichi, Riku starts asking Shunichi some pointed questions. When he finds out the truth, Riku is unable to hide his surprise, but he promises to support the two of them, who clearly care for each other. Meanwhile, Shunichi and Chiyomi learn that there’s more to the story of the thumb-sized princess, and they set out on a trip to turn Chiyomi back to normal. But will everything work out the way they hope?