In the end, he has to sedate Judy and put her to bed. Knowing how deeply Carl had corrupted her and indoctrinated her, Jimmy puts his mother under Suicide Watch. He can do a much better job of taking care of her and the baby then the authorities can, so he goes ahead and uses his immense intellect to cover everything up.
A dead clone of Carl will soon be located, sexually abused and then killed by a local pedophile that Jimmy has decided to frame for the crime. His former best friend will go down in history as yet another unfortunate case of stranger danger, and never darken Jimmy’s doorstep ever again.
It doesn’t fix anything; it doesn’t make everything alright. Shit is fucked, and likely will be forever, until he, his mom, and his sister-daughter can eventually find a new normal together. But Jimmy… Jimmy thinks they can do it. He intends to make sure they succeed, in fact.
After all, he’s Jimmy Neutron. There isn’t anything he can’t do.