Mahiru's backstory, which involves being kidnapped, abused and photographed, developing a second and more violent personality and killing her captor in order to escape. Not to mention that the experience left her traumatized of men and a phobia of the light.
Entire Tokaku's character development subplot. Through the influence of your roommate you go from Emotionless Girl and The Stoic who sees her entire life as a list of objectives to complete - to being considerably more humane and normal. You finally realize that you have to take your life in your own hands and set your goals and objectives by yourself. Yet the first problem you have to solve by yourself in your life - is to decide, was it all real, or it was just the work of some "laws of nature"? Did you really become self-aware and independent,or are you simply deluding yourself? And even worse, there's only one way to check, and that is - to attack your roommate with a killing intent.
If the show hasn't gone for a full HappyEnding, it would be a very sad tragic story. And even with the happy end - it is still a very sad story, just without tragedy. Extra credits go to the final episode, where Tokaku still shows some signs of My God, What Have I Done? towards Haru.
The manga's Chapter 46, counterpart to the anime's Episode 12. Haru, unlike in the anime, offers no resistance and is mortally wounded via a gunshot to the chest as a result. Upon seeing that a heart-broken Tokaku subsequently is attempting to commit suicide, Haru, for the very first time in her life, consciously tries to activate her Queen Bee ability in order to ensure that at least Tokaku can be saved even if herself might not make it.