Ok, I went into some research about how Elfen Lied fully ends in the manga. I know quite a few details, but not all of them.
- Lucy actually has three personalities, Nyu, Lucy, and Lucy2, who appears at the end. Lucy2 is shown in the anime as the DNA talking to her. Lucy2 kicks in and even attempts to kill Kouta.
- Lucy does die.
- Lucy's mom didn't abandon her on purpose. She was kidnapped by Kakuzawa, Lucy's mom got rid of her quickly, most likely in order to protect her. That's when the orphanage found her. But if her mom had kept her, Lucy would have grown up in a nicer childhood and wouldn't have killed like she did, nor would her DNA tell her to.
-Lucy does have a half-brother. After Lucy's mom abandoned her, Kakuzawa fathered the half-brother. It never truly mentions if it was a rape or not.
-Lucy probably had more siblings then just the half-brother. Also Lucy's mom was human, but Kakuzawa knew that all of her children would be diclonii who could reproduce.
At the end after Lucy's death, Kouta keeps his childhood promise. To visit her every year. He visits the puppy's grave. After about 10 years and still visiting, he and Yuka have a child, which they name Nyu, since both Yuka and him loved Nyu and felt extremely bad when she died. One year Nyu, their child, is digging around the grave and accidently finds the bottle Lucy buried there. Which she had put a jade stone, that Kouta had given her, manga only, and a letter. The letter also revealed her true name to be Kaede. Which is also the inn's name and means 'Maple'. She also states in her letter that the jade stone Kouta gave her would have been a nice stone used for a wedding ring, implying her true feelings for him, which she regretted she never got to tell him. Kouta then breaks down crying, which shows he's forgiven her for killing his dad and sister.
Also before I go any further, a vaccination was made for everyone who had the vector virus, and everyone in the world was vaccinated with it, so no more diclonius babies would be born.
Back, to where I was before. After Kouta breaks down crying, two twins come out from behind them. Then Nyu (2), says "Kaede, where have you been?", which right there startles Kouta, because Kaede was Lucy's name. The twins only reply, "We came here to visit a special friend."
When they say that it shocks Kouta and he's still crying, but now he's smiling and he starts to head towards them, that's how the manga ends. Also the two twins, had the bows Nyu use to have tied on their heads, in the same spot horns would be. So you know they are diclonii twins. Everyone may have been vaccinated, but don't forget Lucy had siblings that could spread it again and reproduce. Also it's mentioned that both twins had Lucy and Nyu's memory, including the twin Kaede, was sad and solemn like Lucy while the other one was happy and smiling like Nyu.
The reasoning behind the twins being able to get Nyu and Lucy's memory is, when Lucy2 is about to kill Kouta, two hologram like versions of Lucy and Nyu appear side-by-side and protect him. Also Kouta doesn't shoot Lucy to kill her, he is too upset to do that.
Also in the manga Kouta didn't forgive Lucy like he does in the anime. Not until the very end. There's more to this, but this pretty much explains it all. Look around for more details if you wish. I even have pictures. I'll post a raw picture of Lucy's half brother:
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