After a queen's tragic death, the king abandons his newborn daughter in a cave, but a witch saves her. Years later, the tomboy princess must confront and ultimately falls in love with the enemy king.

Fantaghiro and Romualdo are preparing their marriage when the Black Queen disgusted by their deep love captures Fantaghiro's father. Romualdo and his soldiers go on their journey to free him. But the insidious Black Queen transforms herself into Fantaghiro, makes Romualdo her slave by kissing him and captures the rest of his army. Fantaghiro follows Romualdo although she promised him to stay home, finds the camp deserted and enters the near castle of the Black Queen. When she asks for a duel to free her people she is very surprised to face Romualdo who has forgot her completely due to the magic of the Black Queen.

The powerful evil wizard Tarabas gets knowledge about a prophecy that a king's child will defeat him. So he sends out his army of dead soldiers to kidnap all royal children. When the soldiers attack Fantaghiro's castle to steal the babies of her sisters, the battle seems to be lost until she discovers the secret to defeat the solders but by doing that she loses Romualdo. Now Fantaghiro must find the evil wizard Tarabas and convince him to break the spell and bring back Romualdo.

A black cloud travels across country, kills animals and plants and dries up the rivers. When the cloud reaches Fantaghiro's kingdom she meets Prince Parsel who follows the cloud to get his stolen castle back. After her castle vanishes, too, Fantaghiro joins Parsel on his journey to find her home, her people, her family and her love.

In this last episode princess Fantaghirò ends up in a parallel dimension fairy land full of kids. Here the princess must fight against a villain called "Nameless".