Nell's Primer
The Primer itself can be seen as an allegorical representation of Nell's real life. It portrays the adventures of a Princess Nell who goes through many steps that lead her to becoming a queen. Nell's life and the life of Princess Nell are coordinated, for example, when Nell escapes her home with Harv, Princess Nell is shown escaping her stepmother's dark tower; the mouse army of Princess Nell is Nell's army of young girls who have also been guided by Primers. The story of both Nell and Princess Nell are told side by side, and both stories lead to the same conclusion and that is the defeating of dark forces and becoming a queen.
The Lesson of the Screwdriver
The Lesson of the Screwdriver is a first real-world lesson that Nell learns. Before she escaped her home, she intended to kill her mother's abusive boyfriend with a screwdriver, as the Primer itself told her to do, but then she realized the gravity of that deed and failed to do it. Even though the man hurt her and her brother, and even if his death had made her life better, as was the intention of the Primer, the appliance of what is said in a book into real life proved to be much more complicated.
King Coyote's Wizard O.2
In her final battle, Princess Nell has to defeat King Coyote. But, before that she has to go through his mighty thinking machine, the Wizard O.2. Now, this is not only an allusion to the famous children's novel, but it also has allegorical meaning connected with that story. The Wizard of Oz from the story is a fraud who uses illusions to rule the Emerald City. The machine in this novel, Wizard O.2, is said to contain the entire wisdom of the world and it is greatly feared and respected. But, it turns out that it is only another Turing machine, like the rest in the kingdom, and that it's controlled by King Coyote and its demonstration of power is nothing more but illusion to impress the commoners.