After destroying the Diclonius Research Institute and its island, killing whatever remaining Clone Diclonii there were in the process, Lucy makes it back to the shores of Yuigahama Beach in an escape pod like the one Nana traveled in much earlier in the story. Much to her surprise, Kouta is already there waiting for her, mirroring his and Nyuu's first meeting in the very beginning of the tale. However, whereas he and Yuka warmly took Nyu in, Kouta's meeting with Lucy herself is cold. Though he's still encumbered by his gunshot wound from earlier, which rightly worries her, he demands she not touch him. However, he can't easily walk to the place he wishes to show her, so after giving her his coat, as she's still very much naked, he lets her carry him up to the Sea Candle. In the meantime, Yuka and Mayu first find that Kouta has left the hospital.
He briefly reminisces about how his late sister had wanted to come here when it was completed before asking Lucy directly why she murdered Kanae and their father. Up against her goal of nearly a decade, Lucy struggles but finds the words to at least try and explain this to him. She offers up the existence of the DNA Voice, which she describes as only giving advice, not truly controlling her. She tells Kouta of how Nyu came to be, an effort to co-exist with him safely when Lucy the killer would always present a danger. She finally explains that the real betrayals and pain she had encountered left her so reflexive, that when Kouta seemed like he had lied to hurt her, she killed his father and little sister in order to end her connection to him and all other Humans. This is noteworthy because in other instances, she seemed to describe the murders as simple payback to Kouta or even an effort to cut his ties to others, so that he would focus solely on her. But if Lucy's differing explanations are a mistake on the mangaka's part or part of Lucy's divided mindset (even absent the personalities), she finishes by offering up the best apology she knows how for her actions, even acknowledging it may well not be enough.
While factors such as the recency of his restored memories and the pain from his life-threatening wound might easily have played a factor in Kouta's reaction, in fact it can also be seen as sadly predictable: He rejected Lucy's explanation almost entirely and made it clear he could not forgive what she had done. Despite preparing for this outcome and even stating that she was prepared for it, the impact of this rejection was immediate and apparent for Lucy. In seeming contrast to her nearly trademarked bursts of rage, Lucy tearfully but calmly accepts his judgment. Perhaps unlike times past, this pain was acceptable to her as having a straight line from her own actions, rather than the cruelty and prejudice of others. Further, having done all she did merely to reunite with Kouta and have the chance at an apology, Lucy could not bring herself to harm him. But the boy whose super-power was to always be able to surprise her did so once again, when he also rejected her decision to leave Maple House and their makeshift family forever.
In this sequence, he does take pains to deconstruct her explanations about the influence of the DNA Voice, stating that Humans have this too, but choose to live with and control it. On the one hand, readers know Kouta to be wrong, since many sequences show that in fact the Voice is very real. On the other hand, there is some evidence to suggest that Lucy's troubled mind magnified the role of the Voice far beyond what it was meant to be, perhaps even being another personality, a dark counterpoint to Nyu. Like many other aspects of the series, this notion is left ambiguous. Kouta states that he has no intent of losing Nyu just to banish Lucy, adding in for good measure that he does not wish to lose any more members of his family, period. In exchange for her vow to never kill or cause harm again, Lucy is permitted to stay at Maple House. At her plea, Kouta finally agrees to let her summon medical help and return him to his hospital bed. If Lucy was actually somewhat heartened by her mixed success, she was about to crash hard once again.
Waiting down the lighthouse steps for her was Kurama, her old enemy, gun drawn and determined to end her potential threat for all time. Kurama the would-be cold killer was met by a Lucy who knew the prices of breaking and keeping her moments-before promise to Kouta; she chose to keep it and allow Kurama to end her life, so that at least Kouta's last memory of her would be an honorable one. It was then that the DNA Voice ended at least part of the debate about its nature, usurping control of Lucy's vectors and severing Kurama's arm.
In the happenstance that is part of Elfen Lied's DNA, Kouta had made his way down the steps just in time to witness this seeming transgression, angrily stating that he hated Lucy, whose word he felt he could not trust. While the DNA Voice gloated over being confirmed as right about Kouta, and therefore all humans, it also found that it had overplayed its hand. By revealing it had the ability to override Lucy's will, it had lost the ability to pose as merely a harsh adviser and cast its entire role in Lucy's life into question. Again likely owing to Kouta's hatred stemming from her own real actions, Lucy refused to hate him back. Almost as this occurred, Kurama's obsession met with Kouta's delivery of one last surprise. As the wounded scientist regained his gun and fired on Lucy, Kouta jumped in the path of the bullet. With a second innocent gunned down in his hunt for Lucy, Kurama's part in this drama is done as he is crushed by the realization.
With Kouta's wounds now flatly lethal, he attempts to tell Lucy that he did not wish matters between them to be unresolved, especially with hateful words, as happened with Kanae. As he slipped into a terminal coma, Lucy exploded with rage, tearing the Sea Candle to pieces and sending Kurama flying to his apparent doom. Lucy made the choice then and there to not let the world take anything more from her, and moved to end it all with her unleashed power, even as her body began to disintegrate from its overuse.
The higher echelons of the Japanese Self-Defense Forces met to discuss the situation, and found themselves with next to no options, even the very grimmest. The unthinkable use of the atomic bomb was discussed, but shot down by the American government for the inability to target Lucy with any precision. Arakawa watched the carnage move out from Kamakura and again realized her own role in these matters. Kurama was rescued from falling to his death by Nana, who aided him in tying off his lost arm as well. Humbled and sobered by his wounding of Kouta, he asked Nana to go on without him as she pursued Lucy and sought to aid Kouta. Indeed, all the ladies of Maple House sought to reach and join their friends, even Nozomi, wounded in the attack on Maple House and under the watchful eye of her protective father. Somewhere in her rage and fury, Lucy stopped and realized that she could turn her power to saving Kouta's life. The price for such precision and deep repair of multiple concerns would certainly be her body's remaining cohesiveness, and this solution was fought against severely by the DNA Voice. Lucy ultimately rejected this entity not merely for the love of Kouta, but for how much she feared that building a world just for her meant being alone, a fate she could not abide. With the Voice having revealed its true power against Kurama, it was helpless as Lucy began the draining process, almost a direct life transfer for the effect it had on her.
To focus on the beauty of the world and those she had come, however reluctantly and haltingly, to care about, Lucy sang the poem and song Elfenlied that Nozomi had taught to Nyu. Her voice broadcast unto itself, being heard in ways and in places logic and physics says it should not have been able to reach. Jet fighter pilots who met their doom against Lucy's 'operation room' force shield also heard this over their headpieces. When the song was done, Kouta was no longer dying, but still faced weeks to months of hospitalization to recover. The girl he had known as both Lucy and Nyu was beyond hope. Almost as the other residents of Maple House arrived, he and they saw that Lucy's body had melted, now a pile of oozing flesh, exposed bone and organs, and ready to inform Kouta it was time to keep a dreaded ancient promise.
In a vision, Kouta sees Lucy, who tells him it is as much the danger to the world and her many sins that necessitate her death as the condition of her body. She is filled with regrets, but at least one of these can be put aside if he is the one to kill her. Kouta's refusal is met with a reminder that he in fact promised to do this when they were only children. Lucy urges him to look for her each year at the spot they first met on the anniversary of that meeting. As separate spirit-beings, Lucy and Nyu depart the Earth plane together, leaving only the Diclonius DNA Voice inside the dying body. As Kouta and the others struggle with this loss, a group of soldiers, led by a Saseba operative with ferocious nearly irrational hatred for Lucy arrives just in time to attempt a lecture on the dying young woman just before the Voice unleashes her vectors against them. Nana warns Kouta that the entity now inhabiting the body is neither Lucy nor Nyu. Their spirits appear to him once more, proclaiming that he must now kill her and that their power can only briefly hold back the Voice as it rages.
Kouta takes a gun from a fallen soldier (likely a Desert Eagle, since it matches ones seen earlier) and finally prepares to keep a promise a little boy could barely process and certainly never imagined he would have to fulfill. Yet again he finds he cannot do it, the love he felt for both parts of Lucy staying his hand. The Voice, which had been enraged at her impending destruction, now felt shocked and surprised that Kouta really did love Lucy after all that had happened. It also came to process the amount of pain the ruined body felt, and decided it wished to die. Raising the gun Kouta dropped back into his hand, it begged for him to kill her. With himself and the other ladies of Maple House in tears, Kouta fired and killed the body once and for all, ending the Voice's tormented existence and freeing the spirits of both Lucy and Nyu.
The Lighthouse Incident was a hard harsh denouement to a series known for grim moments, and has weighed upon the mind of many a reader. On the one hand, letting Lucy live would have made all that she had done trivial and forgettable, almost something to be laughed off like Nyu groping her housemates. On the other, it asks quite a bit of the series' fans to simply accept that the protagonist failed and did not gain her one true love. The place Kouta's sister always wanted to see became the place that he dispatched a girl he could have truly loved and even married, but was bound on levels of emotion and honor from fully forgiving for a horrendous mistake whose seeds were planted by neither of them. Many manga and anime and indeed many series might well end right here, this bleak despairing moment that, as Longfellow put it, showed that there was no peace on Earth, and that hate was strong, in the despairing stanzas of his anti-war poem (later a popular song) I Heard The Bells On Christmas Day. Yet just as that poem-song arcs back up to affirm certain positive truths and faith, so is this not truly the end of Elfen Lied. A finale awaits these characters, and for Kouta in particular, a promise Lucy made in the spirit realm will be kept.
At the end of this incident, love does not conquer all. But against an uncaring world, hubris-filled schemers and the foolishness of youth, it does endure, and that is perhaps miracle enough.