The Lighthouse Incident is the final climax of the Elfen Lied manga. In this crucial event, not only does Lucy and Kouta's inevitable reunion finally come into play, but so too does her final brush with the remnants of the Diclonius Research Institute and those working for its sister branch. The incident is also the stage for our protagonist's ultimate death.
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, where he and Yuka warmly took Nyuu 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.
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.
(article in progress, please pardon our dust!)