Kraehe and Mytho have vanished. Princess Tutu helps Fakir back to his dorm and binds his wounds, and when he wakes up they decide to search together for Mytho, though Fakir still refuses to team up with Duck. They search everywhere but find nothing, until they happen upon Edel, who shows them the way. In the passage, Duck is so clumsy that Fakir wonders if she and Tutu can even be the same person. She trips and he moves to save her, and they both ending up falling down a deep hole. Duck reveals to him that she is actually a duck and transforms to find a way to get out. Together, Duck and Fakir go to where the final stage has been set.

Mytho follows a mysterious voice and disappears. Duck and Rue go looking for him. They run into Edel, who tells them a story of a maiden who died and directs them in the right direction, which enables them to find Mytho. He finds the Wili Maiden, the ghost who’s been calling to him, and is offered the rosemary, which will allow the ghost to take him with her to the land of the dead. Rue tries to save him by dancing with the ghost, but fails since the ghost can dance for much longer than Rue. When Rue falls, Duck hides and transforms into Princess Tutu. Tutu dances with the ghost (revealing herself to Rue), and is able to keep going. She gains the feeling of sadness from the ghost and gives it to Mytho. Drosselmeyer notes that the feelings returned to the Prince, thus far, are unhappy ones, and questions Tutu, “Is this how you will restore happiness to the Prince?”

Rumors fly about the incident between Mytho and Fakir. After a second altercation involving Rue, Fakir is banned from the school for a week. It is revealed that because Mytho's heart shard of love had been soaked in Raven's blood, he will turn into a raven when all of his heart shards are returned. Rue and her father need Princess Tutu in order to complete the prince's heart and the Raven warns Rue that she cannot try to make Tutu disappear. Under the raven blood's influence, Mytho asks Pique out, seeking her pure heart as a sacrifice to the Raven. He demands that she love only him and hate all others. Pique and Mytho meet at night where he tries to take her heart, but Princess Tutu stops this by explaining to her that she did not truly love Mytho. Duck returns Pique and Mytho to the school, where she stays with Pique until the next morning. Pique forgets about having loved Mytho and the friendship between the girls is repaired.

(During the original airing, each season 2 episode aired as a half-episode that premiered weekly. This archives the original air-date of part 2)

After the drama club asks Fakir to perform in the story of the Phantom Knight, he begins to dream about him.

(During the original airing, each season 2 episode aired as a half-episode that premiered weekly. This archives the original air-date of part 2)

Distraught over what she has done to Mytho, Duck thinks about giving up being Princess Tutu, but knows that if she does she can no longer be a girl. Drosselmeyer is worried that the story will be frozen again if Duck quits, so he stops time to encourage her. His pep talk, however, achieves the opposite of his intentions: Duck throws her pendant into the river, transforming back into a duck. Meanwhile, Mytho is confused at the new emotions he is feeling and wanders to the river. There, the heart shard of curiosity takes him deep underwater. Duck tries to save him but cannot in her duck form, so she retrieves her pendant and becomes Princess Tutu once more. Mytho tells her that he does not want her to go; that he wants her to restore his heart. Gladdened, Tutu is about to restore his feeling of curiosity when it is suddenly stolen by the Raven Princess, Kraehe.

Fakir, having failed to shatter Mytho's heart, wonders what he should do: should he give up, especially now since Mytho wants to restore his heart? Rue has her own demons to deal with, as she tries to convince herself that there is only one of her. But Rue does not want Mytho to change, so she decides to accept her role as Kraehe. Duck finds another piece of Mytho's heart, devotion, possessing a student artist. Princess Tutu removes the heart shard, but Kraehe appears and takes it from her. Mytho comes and Kraehe's resolve wavers when the one she loves stands against her, giving Princess Tutu enough time to restore the heart shard.

Mytho, inspired by an overheard conversation between Duck and her two friends, decides to give a present to Princess Tutu to express his feelings and to find out how she feels. He goes out to town with Rue, where they find Edel selling gems. Edel gives Mytho a gem called Love, but warns him that although beautiful, it can be dangerous and delicate. Rue, aware of the gem's intended recipient, is jealous and scuffs it, then tells Mytho she will shine it and make it even more beautiful. Instead, she curses the gem with hatred and spells a raven's feather inside before giving it back to Mytho. Mytho gives it to Princess Tutu, who discovers the heart shard of love is inside. She is about to return it when Kraehe's hatred manifests and binds her. Kraehe appears and rips the half-returned heart shard out of Mytho's chest.

It starts with Duck dreaming of dancing with Mytho as herself, not Princess Tutu, until he makes the mark for death and turns into an injured Fakir. Shocked, Duck wakes and recalls what happened when she saved Mytho from Princess Kraehe. Later in the day Duck bumps into Mytho and Fakir and contemplates telling Mytho everything, but Fakir distracts Mytho so she can keep the fact she is a duck a secret from Mytho. In class Mr. Cat tells a story of meeting a legendary dancer in his younger years to explain the importance of practicing the basics of ballet. During the story the still-corrupted heart shard in Mytho's heart acts up, and he later steals the shoes given to Mr. Cat by his role model. Rue speaks with her father, who is revealed to be the Raven from the story, and praises how the raven's blood in Mytho's body is changing him like they wanted. For a second time, Duck transforms into Princess Tutu to save Mytho.

Mytho tries to tell Mr. Cat that Fakir didn't push him out the window; but of course no one believes it. So Fakir and Duck try to wonder what happened to Mytho.

Femio and his wholehearted views on love prompt Mytho to make the mime motion for love. This struggle with his evil self puts Mytho in the nurse's office.

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 learns he is a direct descendent of Drosselmeyer. Fakir is tested to see if he truly has the power.

(During the original airing, each season 2 episode aired as a half-episode that premiered weekly. This archives the original air-date of part 2)

(During the original airing, each season 2 episode aired as a half-episode that premiered weekly. This archives the original air-date of part 2)

(During the original airing, each season 2 episode aired as a half-episode that premiered weekly. This archives the original air-date of part 2)

(During the original airing, each season 2 episode aired as a half-episode that premiered weekly. This archives the original air-date of part 2)

(During the original airing, each season 2 episode aired as a half-episode that premiered weekly. This archives the original air-date of part 2)

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.

Fakir questions why he was able to write Duck's story, but not the one to save Mytho. Duck tries to get Rue to help her find the rest of the shards.

(During the original airing, each season 2 episode aired as a half-episode that premiered weekly. This archives the original air-date of part 2)

(During the original airing, each season 2 episode aired as a half-episode that premiered weekly. This archives the original air-date of part 2)

Duck awakes from a dream in which she is a duckling, watching a handsome prince dance ballet. Later, she walks early into class and discovers Mytho, an advanced class student, dancing alone. When she trips, he dives to catch her, twisting his ankle in the process. Duck wants to apologize to him but is prevented from doing so by Mytho's controlling roommate, Fakir. The next morning, Duck resolves to apologize to Mytho, and spies canary chicks beginning to fly. One of the hatchlings hesitates and is forced to jump when a crow tries to attack it. Mytho leaps to catch it and falls as well. To save him, Duck transforms into Princess Tutu. Mytho asks who she is. Tutu/Duck remembers that she is a duck, and runs away.

The next day, Duck wakes up to realize that she is just a duck. Drosselmeyer appears to tell her that she is also the legendary Princess Tutu; her task is to return the pieces of heart to the Prince, Mytho. Longing to one day see Mytho smile, she decides to take up the challenge. Drosselmeyer gives back the pendant that changes her into a girl, as well as Princess Tutu.\n\nAn Anteater-girl, who is bitter and jealous of Rue for her superior dancing skills, sets her eyes on Mytho. She and Mytho have a dance-off with Rue. Rue chooses Duck as her partner and they win. Duck discovers that the anteater is being influenced by a shard of Mytho's heart—the feeling of bitterness. She transforms into Princess Tutu and convinces the heart shard to return to him. Mytho regains a feeling, which worries Fakir.