how does the masterpiece happen?

so i just finished a6a6a5, and im confused on how it happens. i know the beta kids cant just be trapped in the juju, because theres epilogues, and i dont think they could have an epilogue without the main characters. however, it has to have happened some way, or else john could never get his retcon powers. my current thought is that its a doomed timeline where the trolls died somehow, which would explain why the only ones there were the kids and arquius.