As the conclusion of the Elfen Lied Anime was being planned and animated, script revisions were enacted for episodes 11, 12, and 13. Recently the original ideas and plots were brought to light and will be chronicled here.
(Thanks again to User Yoshik for this invaluable information)
Final Scenario Outline for Episodes: 11,12, and 13
(Collected from remarks by Takao Yoshioka, who oversaw the plot and transcripts for the entirety of the Elfen Lied anime; Dated June 27, 2014; Edited for Grammar, Syntax, and Flow)
"This is the outline of the scenarios finally agreed upon after many twists and turns. However, while people were working on it, the director requested changes to the storyline, shifting from an action-oriented one to the more drama-oriented one. Consequently, I abandoned these outlines and directly re-wrote the transcripts (without re-using some of the plotlines). The scenario outlines here are therefore largely different from the ones actually aired. For Episodes One through Ten, there are no big differences between the outlines and the episodes actually aired, so they will not be covered here."
Some events played out identically to the series as broadcast. Alterations will be in italics.
- In the original script, events played out the same way up to a certain point. Mariko, released from her containment chamber, murders her supposed surrogate parent, Doctor Saito, who while dying, detonates a bomb implanted in Mariko's arm. This sequence was followed by Shirakawa asserting control over Mariko by reminding her of the many bombs still inside her.
- Exhausted, Shirakawa hesitates after releasing Mariko, thinking perhaps she should report it to Kurama. But upon entering, she finds Kurama's office is empty. In it, she finds a letter left behind by Kurama. Her reaction to the letter indicates she is surprised.
- Nana finds her feelings torn; On the one hand, she feels she must deal with the danger that Lucy presents; on the other, the small luxuries and acceptance she finds at Maple House makes her desire not to disrupt it. She hopes that Lucy remains dormant inside Nyu, who she accepts as a good and separate person. Aiding in this judgment are Nyu's sweet but clumsy efforts to give Kouta closure over his grief for his late little sister Kanae. Also, Yuka continues to fear the closeness between Kouta and Nyu will leave no place for her in his life.
- While implicit in the broadcast script, the original script had a scene wherein Nana makes it especially clear to Mayu that her talk of Lucy must be a secret.
- Kurama meets Bando who is cleaning up garbage on the beach. Kurama requests Bando kill Mariko. Bando agrees, on the condition that Kurama repairs his bionic arm. Still reluctant, Bando finally accepts the deal.
- In the broadcast script, Kurama merely makes a generic request for Bando to kill an approaching Diclonius as part of the bargain for his repairs. In the original script, Kurama thinks (in dialogue to himself) about Mariko, believing that finally killing her is an act of love to end her misery and use as a pawn by Chief Kakuzawa.
- In the broadcast script, Yuka observes the closeness between Kouta and Nyu, leaving the house silently and in a huff, only coming back at the end of the episode, having collected her feelings and wondering about the police blockade she saw, including the two detectives she and Kouta met in earlier episodes.
- During the original script, Yuka directly questions Kouta as to whether or not he has romantic feelings towards Nyu. Kouta's response to this is vague, becoming part of what causes Yuka to run off.
- Mariko goes down to the heliport. For the first time, the fully-dressed figure of Mariko, who is sitting in a wheelchair, becomes clear.
- Mariko is given orders to kill the escapee Diclonius, Nana, and to capture Lucy, so long as she is not killed, especially by decapitation. Shirakawa gets a call from Kurama. The specifics about Lucy's capture are absent from the broadcast script; that she not be killed is the only stipulation.
- Yuka tells Kouta that she is going to leave Maple Inn. Surprised, Kouta tries to stop Yuka from leaving, but Yuka shakes him off as she goes. Nyu is continuously trying to repair the grandfather clock.
- Shirakawa is talking with Kurama by phone. She apologizes that she brought Mariko on this mission. Shirakawa was ordered to keep an eye on Kurama by Chief Kakuzawa. But in fact, she has fallen in love with him. She is horrified when she hears Kurama's plan to have Bando terminate Mariko.
- Yuka, after leaving Maple Inn, finds that the nearby streets are blocked. She finds the detectives she once met after Kouta was injured. Feeling something ominous, she decides to go back to Maple Inn.
- Nana is scared by the sense of Mariko's presence and realizes that Mariko must sense her as well. She decides to leave Maple Inn, to spare the others.
- Nana, after leaving Maple Inn, standing face to face with Mariko on the bridge to Enoshima.
- Kouta learns of what's going on from Mayu and helps her look for Nana. (In the original, only Kouta and Nyu came to this scene)
- Mariko is playing around with Nana, stripping her in the process like a doll. Nana pleads for her 'Papa' to save her, at which Mariko taunts that she is going to kill Kurama (not knowing who he is to her at this point). Nana responds in anger by powering up and counter-attacking in earnest. There, Kouta, Mayu, and Nyu appear looking for Nana. Mariko thinks it mysterious that although Nyu has horns, she cannot sense Nyu's approach. Nana tries to let the others escape from that place and tells them to get out. Kouta, failing to grasp the circumstances, starts talking to Mariko. Mariko responds with an attack on Kouta using her vectors.
- Arakawa goes back to the university. She grumbles that she has no time for taking a bath and is forced to look into students' files, trying to find the student who was with her when Professor Kakuzawa was killed. Arakawa finally finds the picture of Kouta.
- Yuka goes back to find Maple Inn empty. Intruders then grab and abduct her.
- When Mariko's vectors are about to reach Kouta, his body is blown clear as if flicked, saved by Nana. Nana is badly outmatched by Mariko. Mariko sadistically toys with Nana. Mariko then further stretches her vectors to Kouta. At this very moment, Nyu changes back to Lucy and helps Kouta.
- Kouta's memories return. He realizes that Nyu/Lucy is the girl with horns that he met that summer.
- The scene of a greatly shocked Kouta, attempting to cope with these revelations.
- Mariko finds her vectors have been deactivated by Nana. Bando, whose right hand is already repaired, is overjoyed to see that Lucy is also in the same place. Nana and Mayu, at the same time, call out to Bando saying "Oji-san" ( a word used for /meaning a middle-aged man), which gets Bando angry, thinking "I'm not Oji-san but Bando!", and shoots at Mariko. Mariko is nearly killed by Bando but thanks to quick action by her control staff, Mariko manages to withdraw. Lucy says goodbye to Kouta and leaves. In the broadcast script, she urges him to wait for her so they can talk one last time.
- Kouta's eyes are wide open, but he is barely conscious. Kouta gets back all his childhood memories. He sees that the one he calls Nyu is the girl he met that summer, and that she later killed his sister and father in front of him.
- Kouta cannot move and is too heavy for Nana and Mayu to aid. As a last resort, Bando carries Kouta. Kouta, who is still hazy, goes with Nana and Mayu back to Maple Inn. They question why Bando is going there, too. Bando hopes going to Maple Inn will cause him to find either Lucy or Mariko.
- They return to find a ravaged Maple Inn. Kouta returns to consciousness, only to learn Yuka is nowhere to be found.
- Yuka is dreaming of crying on the beach, wondering if Kouta loves Nyu. Yuka, not wishing to be angry and jealous, considers herself pathetic. In her dream, Kouta and Yuka are happily married, with Kouta calling for Yuka as the dream ends.
- When Yuka begins to awaken, she is naked and is hung up by her feet in the underground lab of the University. Arakawa prepares a Diclonius virus injection to give to Yuka. The Chief told Arakawa, now that Yuka knew all their secrets (whether she knew any is debatable), Yuka had to be gotten rid of. But before simply killing her, he suggested that Yuka be used for experimental purposes. But Yuka, knowing nothing about the plot, just cries all the time.
- Bando and Nana explain about the Diclonius Research Institute and also about Diclonii to Kouta and Mayu. Everything becomes clear, and it turns out that Yuka was kidnapped by DRI agents. Once again, Kouta awakens to how he cannot live without Yuka, and he hates Lucy, feeling she has caused all the madness.
- A researcher is about to give the Diclonius virus injection to Yuka, but the scientist's head is severed. Lucy appears there. Arakawa is paralyzed with fright and wishes not to die a virgin. Yuka has no idea at all why the one she sees as Nyu is there. Lucy's vectors stretch to Yuka.
- Nana wants help from Bando to rescue Yuka. Bando feels he has no such an obligation and flatly rejects the request. Mayu shows Bando the promissory note of aid he had written earlier, but Bando explains that it only applied once, and Mayu used it up immediately after that. Bando even seems offended that they would try to use it again. At that moment, Nana detects the presence of Lucy. When Nana leaves and then goes to the gate, she finds an unconscious Yuka lying there. Lucy leaves the spot calmly.
- Mariko's vectors are now active once again, and she loses control, enraged at being humiliated. "Everybody, just go to Hell!", shouts a demonic-looking Mariko.
- Shirakawa closes her eyes, pained to see Mariko in such a state.
- Yuka wakes up and learns all about what was going on. Kouta apologizes and thanks Yuka for being so considerate towards him while he was suffering from amnesia.
- Kouta finds himself in a complicated state of mind when he learns that Lucy helped Yuka.
- Yuka says that Lucy must have wanted to remain in her Nyu persona. Kouta feels that he wants to talk with Lucy once more.
- Chief Kakuzawa gets a report from Arakawa that Lucy emerged and helped Yuka. He learns that residents of Maple Inn can be used as bait to lure Lucy. He instructs Shirakawa to send Mariko directly to Maple Inn.
- Nana and Bando are going to fight a decisive battle with Mariko on a cliffside. Lucy emerges there. Lucy protects Kouta, who has been seeking her out, from attack with her body and receives a fatal injury.
- Kurama appears, talking Mariko down and assuring her at last of his love. Kurama holds Mariko as her embedded bombs explode, at last standing together as parent and child, fantasies of a life that could have been playing out before it happens.
- Kouta holds the mortally-wounded Lucy in his arms.
- Lucy: "The only thing I could do is killing people. So many people have been killed because of me. I have no intention to live any longer. I wanted to die as it was but I haven't said it to you yet. So I came back here. Actually, I escaped [from the island institute] in order to tell this to Kouta. I'm so sorry." Lucy apologizes from the bottom of her heart. "I wanted to be ... Nyu ... forever..."
- Lucy breaks her horns off and jumps off the cliff. Falling, she hums the song Elfenlied. (It seems that, at one point, the titular song was to have been in some part of the anime). A scene of Kouta, screaming as she falls.
- A few days later at Maple Inn. Yuka is caring for Kouta who is still bandaged up. Nana and Mayu are preparing a family meal together. Nana says she could get Miso ( soybean paste ) at a bargain price at that shop or another. Mayu, giving a chuckle, responds by saying that Nana now finally learned how to use money.
- Kouta opens the music box. Yuka confesses her feelings for him. Kouta nods, indicating perhaps he has known this all along.
- Around that time, Chief Kakuzawa is about to launch the missile containing the diffusion mechanism for the Diclonius virus. A tattered but alive Kurama appears in front of Chief Kakuzawa. Kurama kills the Chief. The missile is launched, but quickly falls down and the Institute is blown up with it.
- As in the broadcast version, the episode closes at Maple Inn. Wanta is barking. The silhouette of a female guest is seen at the outer entrance. In this version, she actually opens the gate, though it remains unclear whether she is Nyu, or Lucy or someone else. The grandfather's clock starts working. In neither case is the time elapsed between Lucy's apparent death and her possible return stated directly or indirectly.