Darkness hid the pieces of her beloved’s shattered heart, and time is running out for Princess Tutu to find them. Her dream of becoming a human girl has come true. However, peril lurks in the unseen shadows. Using the power of an enchanted amulet, she must unravel a dark and twisted mystery to keep her Prince and herself alive.
Duck meets the lonely-eyed Mytho and is immediately intrigued by him. When he jumps to save a hatchling, Duck transforms into Princess Tutu and softens his fall by placing a field of flowers beneath him.
Duck wakes up and realizes she is a duck again. Drosslemeyer tells her she is also the legendary Princess Tutu, and her task will be to return the pieces of Prince Mytho's tragic heart. She is given a magical amulet which will transform her into Tutu.
Tutu discovers a piece of Mytho's heart--the feeling of loneliness--is with a cook named Ebine who keeps people locked in her restaurant. Later, it is revealed that if Tutu confesses her feelings for Mytho, she will turn into a speck of light.
Duck is still at odds about who she is as Princess Tutu. Fakir tries to figure out why Mytho is regaining his feelings. The ghost of unrequited love, Giselle, tries to take Mytho to the world of the dead, and Tutu must save him.
Mytho is locked in a closet for disobeying Fakir. Later, Fakir becomes suspicious of Duck and aggressively questions her.
Duck collects another piece of Mytho's heart. However, this piece causes him to be afraid of Tutu.
Duck is distraught at having caused Mytho pain. She throws her amulet into the river, but when Mytho needs rescuing she must retrieve it, as she cannot save him as Duck.
Fakir is unable to control Mytho and tries to shatter his heart again. Duck wants to tell Mytho that she is really Princess Tutu but doesn't want him to know she is also a duck.
Rue doesn't want Mytho to change, so she accepts her role as Kraehe. Meanwhile, Tutu retrieves the shard of devotion.
Fakir is keeping Tutu's amulet , and it takes Duck all day to retrieve it. During the retrieval process, Duck witnesses a side to Fakir she has never before seen. Later, Fakir discovers that Duck and Tutu are the same person.
Mytho wants to give a necklace to Princess Tutu, after hearing that giving a gift to someone shows how you feel about that person. A jealous Rue curses the gift.
Mytho has been kidnapped by Kraehe, and the heart shard of love has been removed. Duck and Fakir join together to search for the prince.
Kraehe tells Tutu that she'll give Mytho's shard back if she confesses her feelings. Tutu is prepared to sacrifice herself for Mytho's life.
The Raven's blood in Mytho's body is working according to Kraehe's evil plan. Tutu still does not want Mytho to know her true identity.
Things aren't going well for Mytho. The crow's blood is rapidly overtaking him. To add to the chaos, he jumps out of a window. It is speculated that Fakir pushed him.
Mytho tries to tell Mr. Cat that Fakir didn't push him out the window, but no one believes him.
Femio and his wholehearted views on love prompt the Mytho to make the mime motion for love. This struggle with his evil self puts Mytho in the nurse’s office, where he asks Mr. Cat if being willing to die for someone is the ultimate form of love.
After the drama club asks Fakir to perform in the story of the Phantom Knight, he begins to dream about him. The Knight appears before Duck in the forest. Mytho commands the Knight to kill Fakir. In the fight, Duck is injured but succeeds in returning the emotion of pride to Mytho.
Duck learns that she’s gathered all the heart shards that are hidden in people and now the only ones left are the ones sealing the Raven away. Mytho continues to struggle with what real love is about, even as he tries to get girls to love him enough to give up their lives.
Duck meets a girl name Rachel, who is possibly a sister figure to Fakir. Rachel tells Duck that Fakir used to write stories that eventually came true.
Fakir finds that Aotoa left a book for him. Fakir tracks him down and he is a direct descendent of Drosselmeyer. Fakir is tested to see if he truly has the power.
Duck sets out in search of the rest of the heart shards, but becomes trapped in Drosselmeyer’s world. Aotoa is jealous that Fakir is the chosen one. Fakir has a revelation that the one he must fight is Drosselmeyer.
Fakir sits down to write an order to save everyone from Drosselmeyer’s clutches. Tutu is at Drosselmeyer’s mercy in the world of gears. Kraehe begins to doubt whether Mytho will truly be hers and contemplates shattering his heart once again.
Fakir questions why he was able to write Duck’s story, but not one to save Mytho right then. Duck tries to get Rue to help her find the rest of the shards, but Rue refuses. The Raven is revived and calls on Mytho to offer his heart.
The Raven consumes Rue, but she is still alive inside him. Mytho asks Tutu to restore the final piece of his heart so that he can go save her. Duck asks Fakir to write her story as she goes to return the pendant to Mytho.
The Raven attacks Mytho. Duck tries to help but is unable. Fakir seems only capable of writing what is happening and is unable to change the outcome. Mytho resolves to shatter his heart once more.