So here's what I think. Alice loves Jabberwock a lot, but one day, Jabberwock stopped looking at her and then started looking at other girls. I think this refers to when he somehow used Majokoi Nikki as a "storyteller" to "show people dreams." So Alice was left alone and she couldn't stand the pain and also used Majokoi Nikki as a "reader." She fantasized herself to be the girls in the "stories"--girls who Jabberwock loves. There's that slightly long talk between them which I wouldn't go into, but anyway, Alice suddenly remembers what a magician told them once. "To create an eternal clocktower, she herself must be a cogwheel." I think you're right that she "kills" him. She's like a yandere and couldn't let Jabberwock walk away anymore, and she apologizes for it. Jabberwock accepts her "love" even if he cannot love her back anymore; he is prepared to be with her for eternity. He urges Alice to also become a "storyteller" and create a world as she wishes it to be. Let her "story" become a "dragon" whose roar will shake the heavens.
I wouldn't go into what the terms storyteller, reader, clocktower, etc. mean to me. Frankly speaking, they are also vague to me and I only understand them by intuition as I played the game.