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Born as Kaede, a girl with horns atop her head that resembled cat-ears, she was abandoned in a field on a mountainside, and taken to a nearby orphanage. While she would later be told that her parents abandoned her, in fact only her father did. Her mother, upon learning what he had done, never stopped searching for her.
At the orphanage near Kamakura, Japan, young Kaede was isolated, friendless and taunted for her appearance. The worst of her tormentors were three young boys who called her an animal because of her horns and said that she had no place in this world, since she wasn't 'really human'. Her only comfort during this time, shunned by students and staff alike, was a stray puppy she found wandering the grounds outside the orphanage, whom she fed and cared for. Knowing that the pup would be a target if found out, she told no one about its existence.
After yet another attack by bully ringleader Tomoo and his bunch, Kaede was befriended by a girl who promised to ease her burdens by being a secret-keeper. Needing ever more food to feed the growing pup, Kaede revealed his existence to the girl. The girl may have been loose-lipped or may have intended to betray Kaede all along, but the result was the same. Soon after, Tomoo had the small dog in hand and, while his hench-boys held Lucy, he killed it in front of her, laughing and regretting only that its torment didn't last longer. Enraged by the bullies and betrayed (whether innocently or purposefully) by the girl, Kaede switched (a term used in Dissociative Identity Disorder, "switching personalities") and Lucy emerged, finding that she had the power to create invisible arms made up of telekinetic force. She used these to tear all four children to pieces, almost painting the room with their blood. She left the orphanage forever, pausing only to bury her puppy and apologize for not saving him.
As she prepared to depart the orphanage forever, Lucy was seen by a boy she planned to kill when he mentioned her horns. But to her shock, the boy, Kouta not only doesn't mock her horns, he praises them and states his envy of her for having them. Despite her efforts to push him away, young Kaede (he never learns her name at this time) finds herself becoming friends with the persistent, earnest Kouta, and one day most of all becomes the happiest in her entire life. But the darkness in Kaede stirs up, and at one point she almost strangles Kouta, who she realizes she has fallen in love with. She exacts a promise he cannot understand : to one day kill her, if she becomes a mass killer. In fact she is already becoming this; each night after leaving Kouta, she goes into people's houses and kills the family present, all so she has a place to stay. It is only in off moments that the horror of her actions catches up with her.
Kouta also tells her that the wonderful day must be their last together, as his family is returning home from Kamakura to Hokkaido after the summer festival, which he is attending with his cousin. In a pivotal moment, sensing the fragile emotions of his new friend, Kouta lies and says that the cousin he is attending the summer festival with is a boy. While not meant to hurt her - quite the opposite - Kouta's lie would have hideous consequences. At the festival, Kaede arrived to surprise him, only to see Kouta holding his heartsick cousin and crush Yuka (cousin marriage is legal and accepted culturally in Japan) as she, like Kaede, mourned his upcoming return home. At the sight of this, seeming as it did to confirm her worst fears about Kouta and her grim beliefs about trusting non-horned Humans, Kaede snapped and gave in to an inner voice that seemed to come from her DNA and proceeded to slaughter people at the festival with her powers. An unfortunate witness to this was Kouta's little sister Kanae, who was disbelieved when she related to others what she saw while in hiding.
Kouta's father chose to end their vacation that very evening, and Kaede watched the family's tearful goodbyes with disdain, secreting herself aboard the train and lying in wait. As Kouta got into a heated argument with his little sister over her claims that a horned girl killed the people at the festival, Kaede emerged and called Kouta a liar. When Kanae would not relent from her story, Kouta regarded it as an insult to his friend and told Kanae he would hate her. As Kanae cried and pleaded for him not to say that, Kaede used her powers and split the little girl in two at the torso. Reacting to the noise, Kouta's father had just enough time to see his daughter dead before Kaede cut his head off. As Kouta tenderly held his sister's upper half, he demanded to know why someone he saw as a friend would do something so horrid. Kaede shrugged this off by saying their friendship was the reason he was still alive, and then vowed to kill Yuka as well. This spurred the grieving Kouta to leap atop her, demanding that she stop killing. Somewhere in Kouta's reaction, Kaede finally gauged that he had never meant to harm her, and that her actions had perhaps pushed away the only friend she really had, possibly forever. Fleeing the murder scene, Kaede vows that she will one day be with Kouta once again.
For the next 5 years (one of which Kouta spends in a mental hospital), Kaede traverses the greater Kamakura Area and Kanto region, killing people by way of sudden inexplicable circulatory problems (heart attacks, strokes) and infecting males with a virus that will make their children horned girls like herself, albeit of a different class called Silpelit (Most Diclonius seen in Elfen Lied are Silpelits; Kaede is one of two Monarch-types ever seen or referenced). As the first series of girls so born reach the age of three, their powers manifest, and the girls, aging at twice the normal rate, attack their families, either innocently or possibly out of the same DNA imperative that may or may not drive Kaede. By placing their power emergence at such a difficult age for a young child, the series makes it unclear why these slaughters happen. While Kaede performs no more mass slaughters and keeps out of sight (the cap Kouta gave her hides her horns), her activities do not go unnoticed.
Seeding and capture
At the National Institute For Human Evolution, Doctors Kurama and Kakuzawa had been taking in and finally euthanizing the infant girls that resulted from Lucy's infection of their fathers, trying to determine their source. Since Kurama was among the infected (though not directly by Lucy), his daughter Mariko had been born a Diclonius as well, so his motives were a bit more personal. Working for his colleague as well as Director Kakuzawa, that man's father, Kurama traced back mass killings in the Kanto Region for the last 5 years, coming upon the tragic carnival and finding the deaths similar to ones caused by other Diclonius. He at last learned of the orphanage killings, in which Kaede-Lucy was thought to have been kidnapped by the one who killed the other four children. When a class photo showed a girl with horns, Kurama knew he had found the Queen Diclonius, since Kaede's age meant she predated all other known cases.
In the interim, Lucy had taken a chance and befriended a lonely girl named Aiko Takada who may have had a crush on her, drawing pictures of her from a distance. Lucy chose to defend Aiko from her abusive father and agreed to help her meet her long-lost mother, who was in the same town for an art show. Tragedy struck when Aiko attempted to stop one of her father's rampages, only to (perhaps accidentally) cause his death. Quickly accused of murder, the pair ran off, determined to at least reunite Aiko with her mother. Sadly, while her mother did want to see her again, the pair were cornered by Kurama, with Aiko being shot while trying to protect Lucy. In an exchange for a promise of aid for Aiko, Lucy agreed to surrender quietly. A few weeks later, Lucy was informed by Kurama that Aiko had died. In what may have been a very foolish moment, Kurama, who had shot Aiko, blamed the girls for her death, since Aiko was wanted for a crime and they did not surrender when prompted to. He went further and blamed Diclonius for not wishing to co-exist with Humans. This hypocrisy on Kurama's part was immediately followed by Lucy's vow to hurt him by taking away that which he loved, a vow she would enforce many times against him.
While the timeframe/timeline remains unclear, and relies on an account by Director Kakuzawa, who specialized in deception and misdirection, a result of Lucy's capture (or at least learning of her existence) seems to have been the capture of her mother as well. Her mother, who had never stopped searching for her, was the only female capable of producing 'monarch-level' non-sterile Diclonius. She was held captive and raped by Kakuzawa, which caused her to give birth to Lucy's half-brother, perhaps the only known Male Diclonius. After his birth, she managed to kill herself, and attempts to harvest her body proved fruitless. It seemed that very few outside of the Chief ever knew of the boy's existence.
Escape to Kouta
After 3 years in captivity, Lucy was able to use a suspicious breach in security to escape, cutting a brutal and bloody swath through the guards unfortunate enough to be in her way. Included in the slaughter was Kurama's clumsy but devoted secretary, Kisaragi, decapitated by Lucy as she taunted Kurama about it. Getting outside the building, Lucy was shot in the head by a high-powered sniper rifle, whose shell she turned back but not enough to avoid a serious head-wound. Falling off the island, she was the subject of an immediate search and kill order by Kurama. Washing ashore a beach near Kamakura, Lucy waded out of the waves, nude and reduced to mental infancy. The ones who found her were none other the college-aged Yuka, whom she had never met but once vowed to kill, and Kouta, who, because of his traumatic witness of his family's murder by Lucy, had lost all memories of his late childhood, barely remembering Yuka, misremembering how his father and sister died (accidents and illnesses, changing at times), and in the case of Kaede-Lucy, he had complete amnesia, though she seemed familiar to him. Seeing the girl who had been Lucy was now helpless, Kouta and Yuka took her to stay at a former restaurant and inn owned by Yuka's mother, and leased to Kouta through a maintenance agreement. Based on the only sound the horned girl seemed capable of making, they named her 'Nyu'.
On some level, their awkward and painful past together aside, Lucy and Kouta still knew each other and were each comforted by the others' presence. But the infantile state of the new Nyu personality coupled with her sexual curiosity led to many an awkward moment. Indeed, at times it seemed, in a comical manner, that Nyu was as great a menace to the privacy and dignity of her house mates as Lucy was to their lives. But within hours of the cousins/couple taking her in, the threat of Lucy would come right back into their lives. When a memento of his dead sister seemed to be causing Kouta pain, Nyu broke it, sending Kouta into a rage that scared her off. At first Yuka, and then Kouta himself, went to get her back, with Kouta encountering members of the Kamakura Police Department who, in shades of Kanae, spoke of a girl wanted for questioning, but whom Kouta dismissed as possibly being the gentle Nyu. Finding her back at the beach, Kouta found that Nyu had been seeking a replacement for the lost memento, seconds before he and Yuka were attacked by special forces from Japan's Special Assault Team, led by one of the greatest enemies Lucy would ever have, the ruthless officer Bando.
Lucy's battle with Bando was always one-sided, but not always towards the same side. When it started, the violent Bando was almost repulsed by the passive Nyu, to the point that he handed the matter of her execution to his nervous junior partner, Satou. But his actions against Nyu plus the threat of death were enough to awaken the Lucy persona, who tore Satou apart and maimed Bando, stopping short of killing him only when Nyu once more took over. Broken, humiliated and toyed with by the equally sadistic Lucy, Bando was saved when a young homeless girl living in a beach woodpile shelter bound his wounds and called for aid. After having their wounds from Bando attended, Kouta and Yuka once more found Nyu at the house, with Kouta having been warned by police not to pursue any leads on who attacked him and Yuka at the beach. This increased Kouta's suspicions and made him decide not to cooperate with anyone searching for Nyu. Yuka was at first put off by several awkward moments with Kouta and Nyu, but decided to move in with them when she came to fully realize the depths of Kouta's pain-driven amnesia—with the added benefit of keeping an eye on Kouta and the rambunctious Nyu.
Two New Girls
The young homeless girl, named Mayu, came to Maple House/Inn to return an umbrella dropped by Kouta and Yuka the night of the beach attack. Since she could confirm certain details of the attack (which only Kouta had actually seen), they asked her about it, and offered her food when her obvious hunger reared its head, and even offered to feed her small dog, Wanta. A worrisome turn of events came when a slip and fall once again turned Nyu into Lucy. At first, she grinned as her power rose and moved towards Kouta, Yuka, and Mayu. But the would-be slaughter was stopped as she recognized Kouta from their past together, and withdrew. For reasons either intrinsic to Diclonii or unique to her own past, when Lucy encountered Wanta, she cut the dog's leash, releasing him, though Mayu later found him alive and unharmed. While Kouta and Yuka debated what should happen with Mayu, they also wondered what had become of the girl they called Nyu.
As Lucy, she waited on a scenic stone staircase, pondering her next move, and dealing with seeing Kouta after so long. She sensed the presence of another of her kind, who approached her and demanded that she return to the island facility. This was the Silpelit Diclonius named Nana, who considered herself the adopted daughter of Lucy's nemesis at the facility, Doctor Kurama. When Lucy refused, she also offered Nana her life if she walked away, not wishing to harm another of their kind, who she considered the only true people. Nana's simple devotion to her 'Papa' made this an impossibility, and she attacked Lucy, briefly surprising Lucy with her range and battle-savvy. Her motivation and pain threshhold gave her another set of advantages in the fight, until Mayu, who had left Maple House, not wishing to be a burden, saw the battle, called out and distracted Nana. This enabled Lucy to cut off one of Nana's legs, her pain at last disabling her. Rendering Mayu unconscious (why she didn't kill her is unknown), Lucy proceeded to cut off Nana's remaining limbs, intending to finally behead her. A missed sniper shot stopped her in time. Desperate to protect her "Papa" Kurama, Nana overcame her pain, reached out with her vectors, and effectively disabled Lucy's abilities, which had the added effect of beginning her reversion to Nyu. Enraged at what had happened to Nana, Kurama, not knowing Lucy was helpless, approached her and Nana while the soldiers around them shook in fear from Lucy's reputation.
After scooping Nana up and comforting her while Lucy taunted about his true daughter, Kurama handed Nana off to medics, then shocked everyone present by punching out Lucy, seemingly a suicidal move. Oddly, this blow helped facilitate a stunned Lucy's getaway, since everyone, Kurama included, fully (and reasonably) expected instant and massive retaliation for this attack. By the time the lack of retribution was fully realized, Lucy was far enough away, and Nana's survival was the greater concern. With her vectors disabled, Lucy's personality also faded and soon Nyu found herself bleeding and alone in the woods. Crying, she eventually found her way back to Maple House. Kouta and Yuka resolved to take responsibility for Mayu, whose custody was in effect signed over by her cold uncaring mother. Out of respect to Mayu's wishes, the very sad reasons why she ran away from home were never pursued. While Mayu and Wanta happily became used to their new lives, and Mayu began to attend a new school, Nyu began to learn some extremely limited vocabulary, mainly the ability to say "Yes!". Lucy's persona had vanished for the moment.
The Son Of Kakuzawa
With things on as even a keel as they could hope for, Kouta and Yuka began taking the alternately helpless and hopelessly unpredictable Nyu to university with them, trying to keep a low profile, since they dared not leave her home alone. However, luck or fate kept placing her in danger, even with Lucy out of the picture. She had a nearly comical encounter with Bando, who was on the campus to make a deal that could enable him to fight again. Far darker was when she spoke up during the biology class of Professor Yu Kakuzawa. In fact, it was the Professor that Bando had come to see, and the Professor was also a long-time associate of Lucy's nemesis Kurama, being the son of the Director of the facility where Lucy was kept, and formerly Kurama's superior. Despite Kouta and Yuka's urgings to keep quiet, Nyu drew the acerbic Professor's attention, and he immediately recognized her as Lucy. Also picking up on her infantile mental condition, he deceived and threatened Kouta and Yuka into leaving Nyu with him.
As a stunned Kurama learned back at the facility, the Kakuzawas, father and son, had designs on mating with Lucy and becoming the fathers of the new Diclonius race on Earth, as it supplanted Humans as the dominant species. This drove him to outfit Nana, once scheduled to be killed, with prosthetic limbs that responded to her power, and then sent her away in an escape pod, to await their reunion.
The younger Kakuzawa sedated Nyu, who was crying for Kouta to come back. As he prepared to rape her, the sedative instead awoke Lucy, with her power restored. Turning his peril into an opportunity, Professor Kakuzawa revealed two secrets : That he was the one who had orchestrated Lucy's original escape from the Facility, in order to meet her, and that he too was a Diclonius. Revealing that his hair was merely a toupee, he showed his horns and explained his family history as one of persecution and ancient powers, now diluted away by intermarriage with ordinary Humans. He offered Lucy the world she wanted, with him as her partner in making it. She responded by cutting his head off.
Lucy fled, but already felt Nyu taking over as the drugs in her system wore off. Returning to the college when Mayu pointed out the holes in the Professor's story of being Nyu's uncle, Kouta met Doctor Arakawa, Kakuzawa's assistant and go-fer. She confirmed that the Professor had no brother (a much later plot point nonwithstanding) and guided Kouta down to the basement office, where they found the Professor's body and head. Urged to keep his silence about what he saw, Kouta left in search of Nyu. Their paths separated for a time, with Kouta and Yuka growing closer while they search for Nyu, Mayu reuniting (tensely at first) with Bando, whose life she saved, and Lucy recalling her first childhood meeting with Kouta. When found, Lucy pretends she has found her family and leaves, a lie Kouta will not buy. Ashamed and guilty for her crimes against him, Lucy tries to confess, only to have Nyu take over once more.
Two awkward introductions are made during a brief time of peace at Maple House. The first is Yuka's high school Kohai, a girl named Nozomi. A sweet-natured girl gifted with a wondrous voice, she had an encounter with the overly curious Nyu that bordered on sexual assault, but gained confidence from the support she received there, teaching Nyu the poem/song Elfenlied and eventually came to stay, overcoming intense familial objections to a career as an operatic singer. Taking Wanta for a walk, Mayu encountered Nana for the first time since her horrid battle with Lucy, and when she saw her with four limbs, she assumed once more that what she saw that day had been a delusion. The incredibly unworldly and naive Nana had already met the bionically-rebuilt Bando, forming a shaky alliance with him against Lucy. As Mayu aided her in understanding things, Nana also realized that the girl Mayu called Nyu was likely Lucy, her sworn enemy.
Upon reaching Maple House, Nana was surprised by a playful Nyu, who she saw as Lucy and began to attack. Fleeing when Kouta and the others rallied to Nyu's defense, Nana was again sought out by Mayu, who she failed to convince that Nyu was potentially dangerous. As Lucy and Nyu changed personas while they were recovering from Nana's attack, Nana sensed that Lucy and Nyu were in fact different people. Needing a place to stay and deciding to keep an eye on Nyu/Lucy, Nana apologized for her attack and paid for the damages she caused from money given to her by Kurama.
Very quickly, Nana became entranced by the simple everyday luxuries she was denied while a lab experiment, and even began to like the people who had spurned her at first. To this end, she went to the beach to end her alliance with Bando, not wishing to give up the life that was the happiest she had ever known, while still keeping watch for Lucy's return. But this was disrupted as a task force was flown from the facility to Kamakura, its purpose to kill Nana and recapture Lucy. Headed by two of Kurama's assistants, it was backed up by the most powerful Diclonius of all, Silpelit # 35, called Mariko. This little girl proved more than a match for Nana, who became a plaything in Mariko's hands. But when Kurama returned seemingly to aid Nana, he revealed that Mariko was in fact his biological daughter. The play of emotions and battle had father and daughter at first trying to kill each other, then reconciling. But this would not end well.
Back at the facility, one of Kurama's assistants, Shino Shirakawa, revealed herself to be a spy for the Japanese government and learned of Director Kakuzawa's master plan to infect all Humans with the Diclonius virus. Like his late son, Kakuzawa believed his family were also Diclonius and sought their dominance over Earth. But this plan was too far advanced for anyone to stop, and a phony sattellite launch was to provide cover for the weaponized virus's dispersal. Meanwhile, the Director's son's former assistant, Doctor Arakawa, had an agenda all her own.
Worried about the absent Nana, Kouta took Nyu back to the beach they had left her on, with the infantile Nyu bounding over police barriers to seek Nana. When she arrived, she was seen as Lucy and taken captive, in hopes of convincing the Director to abandon his plans. When that failed and the launch achieved dispersal of the virus, Kurama aimed to remove Lucy once and for all by shooting Nyu. This, however, only revived the Lucy persona, who was challenged by the power of Mariko, who now wished to save her father and Nana from Lucy. Lucy at various points killed many soldiers and taunted that Kurama and Nana were next. When control bombs inside Mariko could no longer be shut down, Mariko went all out, but was taken apart by Lucy's superior skills. Knowing she was doomed, Mariko clung to Lucy as the bombs exploded, shredding her horns and seemingly forcing a permanent change to Nyu. Bando, who had aided in the battle, took charge of the mentally broken Kurama while Kouta guided Nana and Nyu back home.
Over the course of the next six months, Nana settled in at Maple House, which saw Nozomi move in as more or less a regular, and which saw Nyu emerge from her infantile state to that of a reasonably mature young woman capable of coherent speech and thought. No sign of Lucy emerged, though Nyu by instinct retained her habit of groping other women's breasts, especially Yuka's. But in that same time period, the forces that wanted to use and control Lucy had not rested. Moreover, signs of the Diclonius infection started appearing well outside Kamakura, indicating that the Kakuzawa agenda was in full swing, as women far and wide began to concieve babies born with horns.
A Short Peace
At the island facility, Director Kakuzawa revealed to his new assistant, Doctor Arakawa, his late son's assistant, to a gigantic being he called a 'goddess'. The misshapen monstrosity was the highly mutated version of his own young daughter, Anna, who had agreed to operations that geometrically increased the size of her head and brain, giving her probability-predicting powers that were very nearly perfect for seeing the future. But now Anna could no longer live without her head suspended in water at all times. Doctor Arakawa also met the most mysterious and vicious of all of Kakuzawa's operatives, the assassin and sexual predator pedophile called the Unknown Man. Director Kakuzawa set the two with accomplishing a prime task in his conspiracy : Finally recapturing Lucy. The two even made a repulsive wager about who would do it first. But as Kakuzawa schemed, others concerned about him did so as well.
Before being killed by Lucy while trying to get the bombs inside Mariko disabled, Doctor Shirakawa had been Chief Kurama's assistant, but later proved to be a spy for the Japanese government, which had grown suspicious of Kakuzawa's efforts. This organization, called Saseba, had another purpose, to cover up Japan's involvement with Kakuzawa and any secret agendas he might have. After Shirakawa confirmed many of their worst fears prior to her death, Saseba set up another spy inside Kakuzawa's facility. Kurama and Bando, also recruited previously, were out of touch due to Kurama's mental breakdown following Mariko's death, and Bando's continued efforts to prepare for a rematch with Lucy.
The residents of Maple House faced danger on two fronts. At college, Yuka, Kouta and Nyu were cornered by Arakawa, who took Nyu hostage and demanded to know where Lucy was. They escaped when Arakawa panicked after realizing who her hostage really was. At the residence itself, the Unknown Man pushed his way in, killing an unfortunate Diclonius he had tormented and then used as a living tracker for others of her kind. Seeking Lucy, he instead found Nana, whom he disabled before attempting to rape Mayu. Stung by memories of her stepfather, Mayu resisted and made a call to Bando, who arrived just in time to beat Unknown Man within an inch of his life. But when Nyu returned with Kouta and Yuka, Bando realized that Mayu had known all along a horned girl lived there. When his gunshot at Nyu only awakened Lucy, the enemies agreed to settle things on the beach. Nana overcame her wounds and followed, as did Mayu, who wished to reconcile with the angry Bando. But Bando had prepared the beach and stripped it of all debris that Lucy could hurl as a weapon. Combined with some booby traps and other tricks, Bando took away Lucy's advantages in the fight one by one. Just as it seemed he might make the kill, Unknown Man intervened, oddly tender in his pleading for Lucy's life. Lucy then tore off his head and hurled it at Bando, renewing the fight. Witnessing all this, Mayu regained her memories of Lucy's fight with Nana, asking the girl she saw as Nyu what was going on. Lucy, although with regret, then tried to kill Mayu so that she couldn't awaken Kouta's lost memories. Bando saved her by taking the blow himself, shooting off Lucy's regrown horns in the process. Lucy fled as she once more reverted to Nyu. After the three tried to make sense of these bloody events for a time, Nyu found Mayu and Nana and asked if she was really Lucy the killer. Despite her best efforts, Nana found she had to lie and tell Nyu that she wasn't Lucy, lying just as Kouta had done to spare her feelings. Kouta finally found them all, overruled their reasons for staying away, and reunited their family in time for a dinner while waiting on the test results of Nozomi's entrance to music school. Sadly, Kouta, while trying to get information from Arakawa about horned girls, had lead the scientist right to the house Lucy was staying in, which she promptly called in to Kakuzawa.
Meanwhile, a scientist named Nousou had bred four viable clones of the late Mariko Kurama, all outfitted with control devices that kept them docile. Over a thousand other defective clones were used as material in building an Anti-Diclonius tank-like weapon, leading miserable lives until they were harvested for parts. Together with a trained operative/bodyguard of skill and strength, the arrogant, hands-off Nousou was made to lead the home invasion of Maple House to try and recapture Lucy.
The residents were beaten and terrorized by the invading soldiers, while Nana's efforts to defend her home proved futile. When even little Wanta was threatened, Kouta seized a gun from his attackers and held it right at Nousou's head, which got him shot by the Agent overseeing the operation. All the women there were shocked and saddened at seeing Kouta hurt, but Nyu took it worst of all. Without even turning into Lucy, she regrew her horns and tore into the attackers without mercy. By the time Lucy asserted herself, the attackers were in retreat. But Lucy paid a horrible price for this victory, the one she had always feared. Seeing Lucy rip one of the Mariko clones in half, Kouta at last regained the memories of his past, and glared with hatred at the one who had killed his family.
The Pride Of False Gods, The Wrath Of The Real One
At last resigned to the fact that she and Kouta could never be together, Lucy/Nyu said goodbye to Maple House, asking Nana to care for the house and its residents, and asking Yuka to watch over Kouta. As she was leaving, the wily Agent used one of the dying Mariko clones to shoot off one of her horns, catching the other with her gun. Lucy was captured and taken to see Director Kakuzawa, who, through a combination of persuasion and coercion, said that her natural place was by his side. Anna's monstrous form kept Lucy under control, but her power was returning. Kakuzawa then played what he saw as an ace in the hole. He revealed that Lucy's mother had never stopped looking for her, and that her quest caused her to end up his captive. Raping her, he kept her imprisoned until she produced a son, Lucy/Nyu/Kaede's half-brother, whom Kakuzawa offered up as her mate, to keep the new Diclonius line pure. Despites the urges of her Diclonius instincts, Lucy thinks of her friends at Maple House and chooses, even if they would now reject her, to go back home. Determined that all schemes should end, Lucy killed Kakuzawa, her brother, and seemingly the monstrous Anna as well. Lucy taunted the dead Director with a fact the obedient Anna had kept from him : That the Kakuzawas' horns were not like hers, and that all along they had just been Humans with a scalp mutation. But Lucy had problems of her own. According to Kakuzawa, her extreme power use was killing her; In addition, she had to go home and face the enraged Kouta, who now knew full well who she was and what she had done.
Events continued to build and multiply on other fronts. Though Nousou survived Lucy's retaliatory assault, he was killed when Barbara, one of the Mariko clones, who he had released from his control, revealed her rage at how he treated her and her 'sisters', before killing him. Seeking to punish Nana, who Barbara had seen living among Humans, she instead encountered her genetic father, Kurama, who in his madness rejected Nana and embraced Barbara. But when the threat to Nana became real, Kurama reluctantly emerged from his denial and killed Barbara. Reuniting with Nana, the two declared their intent to end Lucy's threat once and for all.
At the island facility Lucy's battle with Anna was seismic in nature, but was enhanced in its damage by two other events. Doctor Arakawa, scheming even against Director Kakuzawa, finished developing and perfected an Anti-Diclonius Birth Vaccine, which would inoculate Human males against siring horned children. The vaccine's presence seemed to have been detected by the thousand-or-more defective Mariko clones held captive beneath the island. Their agitation from this, possibly enhanced by detecting the presence of their queen, Lucy, caused their power to unify and split the island apart from its base to its summit. As the island began to sink, these clones slaughtered every Human they found, vengeance for the hideous and disposable manner in which they were treated. Arakawa for her part kept on the run, clinging to the precious vaccine, Humankind's only hope of survival. In her flight, she came upon another Mariko clone, Diana, still under control and able to be directed to attack her 'sisters', until Arakawa foolishly disabled her control device. Just as Diana seemed set to turn on Arakawa, the Agent who had captured Lucy turned up, put the control device back in, and revealed herself to be the spy sent the Japanese government. When Arakawa nearly fell to her death, the Agent compelled her to let go of her heavy case, only to find it had contained the vaccine that had been her mission to locate. With Arakawa's brain now the only thing containing information about the vaccine, the Agent kept the attacking clones busy while Arakawa went to rendezvous with the chopper that had brought her there. Arakawa felt her heart sink when she found the chopper in flames, the Agent's sacrifice rendered worthless. But Arakawa was rescued by a Vector Attack Craft sent by the Japanese government, a cybernetic tank built from harvested Diclonius. Using the craft's 'Diclonius radar', they saw the clones gather towards something that turned out to be the vaccine case. They recovered it just before the island finally sank, with Arakawa seeing Lucy also escape. A look between the two confirmed that Kakuzawa was dead.
Reaching Enoshima Park Beach in an escape pod, Lucy found that Kouta had left the hospital and was waiting for her on the beach. He was utterly unforgiving and dismissed Lucy's talk of an inner voice driving her to do the horrible things he now remembered. Though he made an offer to let her stay if she never harmed someone again, the Voice inside her (whatever its true nature) seized control when she was attacked by Kurama, whom Kouta saw get his arm ripped off by Lucy. Despite his harsh words, Kouta took the bullet fired by Kurama at Lucy, fearing losing her before they had settled matters, like had happened with his little sister. As Kouta lay dying, an enraged Lucy first unleashed her vectors against the world she now meant to destroy. But she realized that, since she was dying anyway, she could expend herself healing Kouta instead. Healing him enough to put his life out of immediate danger, Lucy turned away attackers on many fronts. By the time Kouta awoke, Lucy/Nyu had melted into a grotesque puddle of flesh and muscle, who reaffirmed that, even if Kouta never forgave her, at least she had a chance to apologize and be with him once again. Once more faced with the loss of a loved one, Kouta vowed that they would find a way to restore her, but both Lucy and Nyu accepted their death and asked that he fulfill his childhood promise to kill her if she ever became murderous on a large scale. Kouta found that he could not do it, even as Nyu and Lucy withdrew, leaving only the demonic voice in their dying body. The Voice-entity casually slaughtered a group of soldiers led by an arrogant commander, and seemed set to destroy Kouta, Yuka, Mayu, Nana, Nozomi and Wanta as they stood there. When the pain of the dying body was too great, and Kouta again refused to kill his old friend, the Voice was moved and itself asked for the mercy of release. Kouta then killed the girl he had called Nyu.
The series' finale recounts a devastating war occurring as Kakuzawa's plans to seed the populace with Diclonius children bore fruit, but details are sparse. A narrative from Kouta related that the deaths caused by these new horned girls plus a cautionary planetwide birth ban until the vaccine was distributed placed Humankind very near to extinction. During this time, Kouta married and had a daughter, also named Nyuu, after his friend, who greatly resembled a younger Yuka.
On the tenth anniversary of Lucy's death, Kouta kept a promise to meet her at the spot where they first met, a promise he honored but had long since given up hope of somehow seeing realized. Little Nyuu found a bottle buried near the spot where Lucy had buried her puppy, containing a keepsake Kouta gave young Lucy, and revealing (to him and first-time readers) the girl's true name - Kaede. There was also a note that confirmed for Kouta that their feelings for each other were not a lie or a fluke.
Little Nyuu then spotted two of her friends, twin girls with large hair ribbons, one of whom was named Kaede. As Kouta turned to look at them, the angle was unclear but seemed to show the girls as being the reincarnations of both Lucy and Nyu, who told him they had been waiting for their special friend. No explanation was given for how this occurred.
The anime version of the story, of course, cuts out significant amounts of backstory, combining and simplifying others. But for the most part, the pivotal events are close to identical to the manga source material right up until Mariko arrived in Kamakura. Instead of a battle where she can utilise her superior experience and cunning, Lucy engages in an all-out fight with Mariko, which the younger but vastly more powerful girl wins, even breaking one of Lucy's horns.
Lucy's nemesis Kurama chooses to die with his daughter when her internal bombs explode, and Bando is beaten again but spared by Lucy. Kouta is still unforgiving in the anime, once his memories return, but vastly more tender saying he still loves the lonely little girl he met so long ago. An angry Director Kakuzawa sends out one more force to face Lucy, which seems to kill her, but nothing is made clear.
Kakuzawa also reveals his horns to a badly confused Arakawa and indicates his plans are far from done with. Some months later, the residents of Maple House are happily rebuilding their lives when a knock comes on their yard-way door. The image behind the door heavily indicates that this is Lucy, but no confirmation is given. A second anime season to resolve these events (for some fans a chance for Kouta and Lucy to reconcile somehow) is among the most requested follow-ups in all of anime.