[[WMG:[[Manga/DeathNote Light Yagami]] killed Misaki's father.]]
Think about it. Those who dare to stop Kira are declared as evil; well, Misaki's father is an example, so Light has killed him when Misaki is a kid.

[[WMG:Misaki's transformation is just a DreamApocalypse.]]
When the real Misaki is seen, she is in a suspended chamber. Her transformation into a Ghoul appears to be a messed up reality. By the way, the hallucinations justify this.

It is revealed that after failing the academy for acting like a ditz, she begins to search for help and finds a program that involves into going into a suspended chamber. As a result, she commits suicide and her body is placed in that chamber, triggering the events.

Even though the glitch can be fixed, Misaki has to decided whether to continue living in a dream or back to reality. For the latter, she has to be killed.

[[WMG:Misaki has been dead all this time.]]
It turns out that a Ghoul has managed to kill Misaki and has taken over her body. However, at some time, it begins to have redeeming qualities.

[[WMG:[[Manga/ElfenLied Lucy]] killed Misaki's father.]]
Maybe he's involved with catching Lucy before Misaki is born?