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The Fentons were successful in prying Phantom away from their boy, but that didn't mean that the damn ghost didn't come back to kidnap Danny while he was recuperating from the operation that depossessed him.
Or, the one where Phantom and Danny are permanently separated by their parents, and Phantom feels like he must protect his human form at any cost, even if they have to flee their home in Amity Park.
(Phantom wants protection, for himself and his human half. He's in search of foster parents to replace the Fentons and will evaluate potential candidates with a keen eye.)
(Human Danny has long since determined that his ghost half has gone nuts after what their parents did to them, but they do need help, so he pushes for Phantom to consider other heroes as potential candidates for parenthood.)