Re: elfen lied
One of the few anime I liked.
Not sure what the bonus episode was about, but the truly final episodes are that, Kohta realises Lucy is the girl from his childhood, he remembers once blocked memories of her murdering his family in front of him out of jealousy, he basically starts hating her, and if memory serves he hits her a few times, all while she is crying and appologising, she hugs him tightly and kisses him to show her old crush on him never left, he then forgives her, she walks off to let herself me shot down in order to prevent her from hurting Kohta anymore, and to stop her "On the run" life.
Kohta and Yuka presumably start going out together.
This is all going by memory of an anime I haven't seen in at least a year, though I know the memory is good, as this, Death Note, Hellsing and Soul Eater were the only Anime Shows I liked. And therefore remembered.