Summary of the entire movie:
Jax abstracts offscreen very early in,
Crew wants to figure out how to stop his rampage,
Pomni decides to enter his mind,
Pomni learns everything about what Jax knew,
Caine comes back, restores Scratch in a new circus instance (confirming abstraction is not permanent)
Caine straight up asks Pomni "hey do you want me to take care of Jax?"
Pomni is like "Not right now, we've found a solution that works.
(Side note, it's hilarious that Pomni doesn't understand that Caine means bringing Jax back, she probably just thinks he means putting him in the basement.)
Gangle and Zooble have lesbian sex, we learn about the identities of the real people the scans are based on, and in the post credits we see all 6 of them getting on a bus, probably back to C&A so they can check what's been going on. It's probably all an experiment or something.
They all stay in the circus because it's impossible for them to leave, they're sentient but digital. The digital circus is like a flea circus.