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.
(article in progress, please pardon our dust!)