The anime follows much of the same story laid out in the manga, yet with some critical differences owing to a differing story structure, time constraints and the adaptation's need to tell a story that varies from its source.
Lucy's parents are only mentioned once, in passing, and only in how someone left her abandoned in a field, specifically a thicket. Dialogue from Kurama places her birth as being unique because of her survival and endurance. This same scene describes other children born like her but dying soon after. This assertion could refer to infants born in modern times, or it could refer to the so-called Original Diclonii, ancestors to the series' villains, the Kakuzawas. This distinction is never made clear.
While the scenes in the orphanage leading up to the killing of Lucy's puppy are mostly identical, the bullies use a flower vase as their bludgeon, rather than a rock. Rather than learning Elfenlied from Nozomi, who is not present in the anime, Lucy hears Lilium from a music box Kouta purchased.
Lucy's capture is similar to what is seen in the manga. However, it is never shown how she met Aiko Takada or why exactly she is on the run. It is also unclear how many, if any, people she has killed during the 5 years she avoided capture.
Lucy's escape from the Diclonius Research Institute is directly from her holding area here, where in the manga it is during an attempted transfer from one holding area to a new one. Also, the anime directly shows a hidden mastermind behind Lucy's break-out; the manga merely plants broad clues that there is one.
Whereas Mayu's encounters with Lucy in the manga (before the murder attempt on the beach) were fleeting and uncertain (for Mayu), the two have at least one very direct encounter. Mayu thinks she is dealing with Nyu but seems to have a sense of some danger when breaking up a potential new clash between her and Nana.
Mayu and Nana both witness the result of Nyu's attempt to dress and act like Kanae in the anime. In the manga, they are only there after this scene has already taken place.
In the anime, Lucy's quest ends after Mariko arrives. Here, she unlocks Kouta's repressed memories on purpose by humming Lilium while slaughtering an entire battalion of soldiers right in front of him, not to mention her method of killing Shirakawa, splitting her in two like how she killed Kanae. However, before she could directly confront Kouta, she was interrupted by Bando, bent on taking revenge on her. As the night falls, Lucy has, once again, defeated Bando in combat. This time, Lucy merely ignores his taunts and leaves him broken, but still alive. Later, she confronts Mariko and is soundly defeated by her, losing a horn in the process, which left her in a state of shock. Lucy woke up just in time to see Kurama die alongside his biological daughter.
After seeing her long-time nemesis perish, Lucy, in a shocking display of empathy, saves Nana's life from Isobe and urges her to go live the life she knows will never be able to have herself. Lucy finally reunites with Kouta at the top of the Jouju-in Temple staircase, in which Lucy proceeds to declare she was born as an agent for human extinction. She also states that, given five years, she can ensure more Diclonii being born than Humans. Lucy is unwilling to do so, her love for Kouta being the primary factor. She then prepares to leave but is stopped by a desperate Kouta, who, while making it clear that he could never forgive her horrible deeds, just wants the carnage and suffering to stop, all while declaring that he still loves her. After a tender scene where Lucy kisses and embraces the only (currently living) person ever to show kindness to her, she departs to confront a much larger number of soldiers, losing her second horn in the process.
An unspecified amount of time later, the residents of the Maple House are greeted by a surprise visitor, strongly implied to be Lucy herself. This possibility gets lampshaded by Wanta's sudden barking, the ceasing of the music box, and the unexplained start of a grandfather clock Nyu had taken to tinkering with before she left.
Because the anime ended after the Mariko storyline, events like Nyu maturing were never brought up. Even if Lucy returned to Maple House, Chief Kakuzawa and his agenda remained an ongoing threat to everyone.
Manga vs. Anime
Aside from the above-noted differences in the anime's story, there are other, Lucy-specific differences between the manga and anime.
- Unlike in the manga, Lucy's vectors number only at four and are limited to the 2m range in the anime.
- Lucy's age is shown briefly in the anime during a screenshot of a data file Kakuzawa has for her. This sheet also reveals she has a height of 162 cm (between 5'3"-5'4") and weighs 48 kg (106 lbs), which is underweight for someone her size.
- While still pink in the anime, Lucy's hair color is a darker cerise than the cotton candy pink of the manga. In the anime, her pink hair becomes the default for all Diclonius characters, only varying in tone.
- Another change from the manga to anime is her eye color. In the manga, the eyes of Lucy, Nana and Marino are mostly colored black but have a greenish hue. Other Diclonii eye colors remain unknown in the manga. In the anime, her eye color changed to red as do the other Diclonii.
- In the manga, Lucy never actually reveals her horns to Aiko. Her hat stays on the entire time the two interact.
- The name Kaede never appears in the anime, where in the English dub Kaede House is sometimes called Maple Inn except for one instance where Kouta directly calls it "Kaede House."
- Lucy is portrayed as more sympathetic and her demeanor is more subdued in the anime compared to the manga. For example, some of Lucy's more harmful behaviors, like engaging in maniacal/psychotic laughter while killing or dismembering people, are absent from the anime, where she is stone-faced the entire time and rarely smiles or laughs. Also, there is more attention paid to her showing remorse for what she's done to Kouta when she's in control and not Nyuu. This alteration could be a result of the anime director Mamoru Kanbe and his desire to pair Lucy with Kouta, as he interpreted Elfen Lied as a love story.
- Lucy's kill count is much smaller in the anime compared to the manga. Her confirmed kill count in the anime is in the 60s, vs. a confirmed kill count in the thousands in the manga.
- Lucy's primary reason for fighting Mariko in the manga is to bring suffering and torment to Kurama as a part of her revenge against him. This idea was not Lucy's motive in the anime during her fight with Mariko, in which she appears almost selfless, stating her desire not to involve anyone else in their battle.
- Although perhaps still present, the "DNA Voice" is never explained to be a real, independent entity in the anime. Its only appearance in the anime is during Lucy's psychological breakdown in her childhood flashbacks, while in the Manga it is a prominent personality that eventually grows to possess Lucy herself by the end of the story.
- Concept art of Nyu shows she (and, by proxy, Lucy) was originally meant to look somewhat different. This art shows her with light brown or dark blonde hair, similar to Yuka's hair color in the manga, an ahoge, and with more angular, even alien-looking horns. Okamoto's notes on this concept art say he forgot to add her right hand (though based on her pose, the hand is present in the drawing).
- It isn't clear how Lucy came to know her parents abandoned her in the forest in the manga. Presumably, she overheard the teachers in the orphanage talking about it or heard the other students talking about it after they learned of it from the teachers. In the anime, Tomoo taunts her by saying "they found [her] all alone in a field," but it isn't clear how he found this out.