The war between the Levamme Empire and the Amatsukami Imperium has been raging for years. In the midst of this struggle, the prince of the Levamme Empire declares his love for Juana del Moral and vows to end the war in one year, as part of his marriage proposal. When the Amatsukami catch wind of this, they assault the del Moral residence, targeting Juana's life. As a last-ditch effort to bring the prince his bride, the San Maltilia Airforce employs a mercenary of mixed blood—a bestado—to fly Juana to the prince in secret.

As a group of university students go out for a night on the town, a sophomore known only as "The Girl with Black Hair" experiences a series of surreal encounters with the local nightlife – all the while unaware of the romantic longings of "Senpai", a senior student who has been creating increasingly fantastic and contrived reasons to run into her in an effort to win her heart.

Mirai and Liko come to the human world to play, but are separated when the witch Sorcierre and her servant Trauuma suddenly appear. Their aim is to acquire the tears of the 44 Pretty Cures, using them for her Most Evil Magic. Only the friendship of all 44 Pretty Cures will allow them to protect the world.