Haruka Haruno, a young girl who wishes to be a princess, meets a strange boy named Kanata who encourages her dream and gives her a special charm. Several years later, Haruka enrols at the prestigious Noble Academy boarding school, where her new roommate, Yui Nanase, shows her around the campus. Whilst hiding in the woods over her embarrassment over revealing her dream, Haruka comes across Puff and Aroma, two fairy siblings from the Hope Kingdom. Just then, they are approached by Close, an emissary from the evil DysDark organization, who traps Yui's dream of becoming an author in a Gate of Desperation to create a monster known as a Zetsuborg. As Haruka becomes determined to protect Yui's dream, her charm turns into a Dress Up Key, which Haruka uses with the Princess Perfume the fairies brought with them to become the Princess Pretty Cure, Cure Flora. Using her new powers, Haruka manages to defeat the Zetsuborg and rescue Yui. Afterwards, Puff and Aroma reveal they were sent in search of the Princess Precure by Kanata, who is revealed to the Prince of the Hope Kingdom.

Puff and Aroma explain to Haruka, they got separated from Kanata after the Hope Kingdom was attacked by Dys Dark, led by a witch named Dyspear, entrusted with finding the three Princess PreCures who possess the Dress Up Keys. As Haruka decides to train hard to become a proper princess, student council president Minami Kaidou finds a Dress Up Key washed up on the beach. After observing Minami's graceful elegance, Haruka asks her to teach her how to do ballet so that she can become more princess-like. Despite the strictness of the lessons, Haruka continues to work hard, only to end up spraining her ankle whilst attempting an advanced move. While treating her injury, Minami confesses that she is far from perfect, only possessing her ballet skills from training hard as a kid, expressing her joy that someone asked her for lessons. Later, as Close targets a boy yearning to be a soccer star to create a Trophy Zetsuborg, Minami spots Haruka transforming into Cure Flora as she goes to fight against it. With Haruka's sprained ankle leaving her at a disadvantage, Minami's desire to protect her gives her the ability to transform into Cure Mermaid and defeat the Zetsuborg. Just as Haruka and Minami are about to celebrate their new partnership, Puff and Aroma discover that the third Princess Perfume in their possession has gone missing.

Haruka and Minami discover that Kirara Amanogawa, a fashion model who has also enrolled at Noble Academy, has the missing Princess Perfume in her possession. Curious as to if she is the third PreCure, Haruka and Minami go into the city where Kirara is working to try and talk to her. However, they are interrupted when Close appears with a Camera Zetsuborg, which the Cures quickly defeat. Before the Cures can properly explain themselves, Kirara just straight up returns the Princess Perfume and leaves. Convinced that she is still potentially a PreCure, Haruka and Minami go to her fashion show, where Haruka gets to know about Kirara and her dreams. As Kirara goes out wearing a Dress Up Key she found, Close targets another model to create a Fashion Zetsuborg. Determined to protect her show, Kirara stands up to the Zetsuborg and gains the power to become Cure Twinkle, allowing her to defeat the Zetsuborg. After the battle, however, Kirara returns the Princess Perfume yet again, stating she is too busy to become a PreCure.

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