After being admitted into the Kaede Inn, Nana is unsure how to contribute despite her best efforts. Meanwhile, she is concerned about fellow resident Nyu, whom she knows as Lucy, a Diclonius with a history of violence that still haunts Nana. She fears that Nyu may harm those close to her and faces the dilemma of either living peacefully alongside her or eliminating the source of her worries, potentially damaging relationships formed at the inn. As Nana grapples with this decision, Nyu recalls a painful memory involving one of her closest friends and greatest rivals.
Taking place within the events of Episode 11 of the TV anime, the Elfen Lied Special combines an anime-exclusive story and a flashback arc from the 10th volume of the manga it is based on.