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"Dyeing Indigo" is the 26th and final episode of the season "Two Mirrors" and the 52nd episode from total.
After the death of her brother, a grief-stricken Hotaru sends Takuma to Hell, promising to follow him so he won't be alone. Both arrive in the Realm of Eternal Twilight where Hotaru insists to Ai that the banishings will stop when Takuma is banished. Ai questions her beliefs, but Hotaru still pulls the string. Ai begins to ferry the crying Takuma to Hell. A smiling Kikuri sits in front of him and offers him candy. Her eyes reflect the four lights seens in the "giant jelly fish" form of the Master of Hell. As Takuma cries and Kikuri taunts her, Ai recalls her own death. She stops rowing when he asks her to help him.
The scene shifts to Hotaru standing in front of a lake. She calls to Takuma vowing to join him soon. The scene shifts then to Wanyūdõ, Hone Onna, and Ren Ichimoku sadly discussing the tragedy. Kikuri appears in a light announcing that Ai could not banish Takuma and turned her boat around. A smiling Kikuri claims to have no idea what happened to Ai as a result. Takuma awakens in the mortal world and sees Ai lying near him dressed as she was when she was sacrificed. When he tries to rose her, she cries that "it hurts," and directs him to hurry towards the lake. He finds Hotaru's abandoned computer and finds her lying on the bank. As he runs to her, Ai walks visibly exhausted.
Ai's companions demand Kikuri tell them where Ai is. She repeatedly protests, then falls silent as Wanyūdõ holds her up, then her forehead splits open to reveal a third eye. She then speaks simultaneously with her own and the voice of the Master of Hell: "You wish to know?" She rises into the air as a large spider's web forms behind her. They--the voices of Kikuri and the Master of Hell--explain that she "turned her back on the law" by returning Takuma, and her souls and the souls of her parents "will wander aimlessly in darkness for all eternity." Her companions argue and beg on her behalf to forgive the one soul she failed to deliver in over 400 years. The Master of Hell announces that Ai is no longer "Hell Girl" and will return to "this world." Wanyūdõ realizes what this really means: "her body will be subjected to 400 years of time all at once. . . ." The Master of Hell disappears commanding them to watch over her.
A woman's body in indigo colored cloth lies curled up at the base of a nearby tree. From a branch hangs the spider form of the Master of Hell.
The peope who attempted to murder Takuma and Hotaru arrive in their cars. They find Seiichi Meshiai's crashed car. Ai's companions watch as some stay to search the area for survivors.
The commercial breaks opens to a weeping Takuma holding Hotaru. Ai kneels gasping nearby. Eventually, Takuma lets go of Hotaru and begins to walk away. Ai demands to know what he is doing then demands he not do what he is going to do. Takuma responds he always held himself in check because his father told him not to seek revenge, but he will no longer hold back. As he runs away, Ai can only stagger saying his name.
In their car, the Hasue family receive a call that Takuma has been found. Yasuharu frenetically scratches at the tattoo on his right chest. Meanwhile, Ai very slowly walks the road then falls exhausted. Above her, her companion fly over her with Wanyūdõ in the form of his carriage. When they come to her, she asks them to move out of her way, and she continues to stagger down the road. Wanyūdõ concludes that her memories as Hell Girl have been removed: "This is the Hell we've been sentenced to. Our ties have been severed."
The scene shifts to Takuma running back to the Hasue home with gasoline. He starts to spread on the outside walls when they and the rest mob pursuing him finds him. Undaunted, he tosses gasoline on them. As he lights a lighter and they ask him if he knows what he is doing, he angrily responds that he does: they will all go to Hell. "Unnamed Mob Member 1" tries to grab him, he bites his hand, and as a result the lighter falls into a puddle of gasoline. As the Hasue house burns, the mob raise their sticks to attack him, but Ai arrives demanding they stop. They all, including Takuma, recognize her. She begs them not to kill Takuma and come to their senses. Watching from a distance, Hone Onna turns away, but Wanyūdõ insists that they much watch. With great difficulty, Ai approaches Takuma, takes his hand, and tells him he must leave. For a brief moment, she smiles at him.
Before they can get far, Yasuharu runs up to them from behind with a shovel. Ai recalls the villager her beat her and her parents. He beats her declaring he will not go to Hell. The rest join in beating her. Her companions can only watch, but her face is calm. From a roof, Kikuri watches without any visible emotion. The mob finally stops when Takuma screams at them. For a moment, the individuals appear horrified at what they have done. Ai turns to him and says, "with this it will end. With this. . . ." Her body dissolves into a shower of luminescent sakura petals that fly into the sky. Watching from her roof, Kikuri silently cries.
The scene shifts to Kikuri standing in the boat as the oar appears to move on its own. The "Giant Jelly Fish"'s tentacles, from this perspective, move with the oar. The boat approaches the gate to Hell over which is the roots of the tree that hold the skeletal remains of Ai's parents. They dissolve into light which ascend into the sky as the roots dissolve into a green light and pass through the gate. With an emotionless expression, Kikuri declares, "It's done," and looks down to see a single cherry on the boat's seat. She kneels down, touches the cherry, then rhetorically asks, "So this was the answer that you chose, huh, Ai? You did good."
The scene fades after the boat sails through the gate to the lake in the mortal world. In a voice-over, Wanyūdõ explains that Seiichi Meshiai's tapes were released to the media which proved Takuma's innocence. Hone continues that those who tried to frame him fled the town over scenes of homes and shops of the village of Lovely Hills closed and up for sale. Ren continues that no media took the "Hell Link" seriously.
The scene shifts to the Realm of Eternal Twilight. Ai's companions wait while her grandmother continues to spin her wheel. She stops suddenly, then addresses them stating that, "Ai said, 'thank you,' you know." As her "thank you" repeats the background dissolves with the three standing in an intersection of Shibuya. Smiling, they part ways to explore the world as the end music starts. During the credits, Tokaru is seen running to greet his father in a park. His father still uses a crutch and has been recently discharged from the hospital. They both visit Hotaru lying in a hospital bed, presumably in a vegetative state. They leave and walk down a corridor and pass a girl in a school uniform carrying flowers. Her phone rings. She looks to see a text message from Hell Girl saying that her request has been accepted.
- Like the previous season, the name of the episode is the same as the season's ending song.