Picking up at the very end of the manga, Lucy/Kaede, on the brink of death, promises that if she were to be reborn, she would be a good person the second time around. Her wish is granted by a God-like entity, who hits the Reset Button on her life, with the intent to change certain key events of her life to revolutionize her existence as a whole.
From there, the story of Elfen Lied restarts, with several differences; Kaede is found and taken back by her mother, Nyu manifests as her twin sister rather than a Split Personality, Lucy also manifests as a separate entity, and things go on from there.
The author has written two other stories set in the same universe: Another Side, Another Story, meant to serve as a "patch" to The Butterfly Effect, and Envoy of the Beginning, a sequel set eighty years into the future.
Currently under construction.
The Butterfly Effect contains examples of the following tropes:
- Abled in the Adaptation: Downplayed. In the original manga/anime, Nana's arms and legs were all severed by Lucy, forcing her to use Artificial Limbs. Here, after the limb severing, Kaede and Nyu come across Nana and try to heal her, but only manage to reattach one arm and one leg before Kakuzawa's men show up and force them to flee.
- Adaptational Jerkass: In the original manga/anime, the orphanage girl who sold Kaede's puppy out to the bullies pretended to be remorseful over it, only to secretly smile behind her tears. Here, the girl, named Rika, doesn't even try to fake remorse and openly tells Kaede she finds her disgusting, following up with a minor Did You Actually Believe...? over how Kaede actually believed she would want to be friends with her.
- Cry into Chest: In chapter 3, Kaede cries into the chest of her mother Mikomi, pouring out all of her accumulated sorrow.
- Heroic BSoD: In chapter 15, after the murder of Mikomi, Kaede succumbs to depression, not bothering to attend school and taking her sorrow and anger out on any gangs and delinquents she can find. Helping Aiko reunite with her mother the next chapter helps her snap out of it.
- Spared by the Adaptation: Aiko Takada survives and is taken in by her mother, unlike canon. Ultimately subverted with Kaede's puppy, who nonetheless lives far longer than he did in the original manga.