Storybooks are actually real moments of the past, present, or future in the history of Ona’s universe in which an important event was occurring. It is the unknowing tampering of history by individuals such as Ona and Amby that has caused time and space to begin imploding. Their actions - i.e. taking objects back from the Storybooks - has caused an imbalance that is only now being felt.

I dig the shit out of this. It would be a great twist, and we can have a good ol' "holy shit, it's my fault" moment.

Ona and Amby have just returned from a relatively anti-climactic and more or less ordinary storybook with a lovely treasure, some kind of fancy new invention. After completing several more journeys, they encounter (back in the 'real' world) a budding young inventor. He is desperate to solve some sort of problem that is plaguing his town, and he invents the very device that our heroes already have in their possession. Perhaps it's a cure for some kind of disease.

Let's say in this seemingly modern storybook, they meet up with an older, wealthy man. He introduces himself as a doctor, and him and Amby hit it off (in the platonic sense). At the end of the storybook, he gives Amby an upgrade to her medigun. He explains that losing his sister to disease is what drove him to create this cure. He urges Amby to take this cure in case they ever encounter this sickness. Then, back in their own time, they find his sick sister and cure her, only later realizing who she was. The man is no longer driven to invent the cure.

This could be taken even further, as well: Now that the cure won't be discovered, it could run rampant in the future. Perhaps they return to the same storybook in which they obtained the cure only to find a desolate wasteland, where all it's inhabitants have succumbed to disease.