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Uncle Scarecrow AU!
So Jonathan is either Maddie's Half brother or Cousin and was really close with the Fenton family until he went a little crazy.
His obsession with fear is driven partially by the idea that ghosts feed on fear and partially since he's ecto contaminated and also feeds on fear to some extent.
Eventually word gets out to a few people that Danny is Phantom and the GIW managed to destabilize him in a way that he doesn't look as human and needs a large amount of fear and ecto to look even somewhat normal.
Maddie and Jack send him off to his Uncle Jon knowing that Gotham has ecto and fear in abundance. Jon digs deeper into his fear gas and figures out that it can work as a stabilizer for Danny if he inhales, drinks, or gets it injected into him.
The Bats get suspicious when Scarecrow breaks out of Arkham and just isn't seen for weeks. They manage to track him down and see him with his mask off in a lab with Danny and Bruce, Tim, and Cass listen in:
"Are you sure this will work, Uncle Jon?" A boy with white hair and Lazarus green eyes asks looking just a bit too inhuman to be comfortable. ("Uncle Jon?)
Crane spins around
"It has to work, Danny and I'll keep working until it does." He approaches Danny with a syringe full of fear serum. The Bats get ready to intervene but the boy doesn't seem scared
"So this chemically causes fear and hallucinations. Right?"
"Exactly. Since you're half human I'm unsure how much fear you're supposed to ingest to stay healthy but we're going to figure it out. Your parents entrusted you to me so I'm going to make sure you're okay." The boy sighs and gestures for the needle. As the Bats shift, this child has to feed on fear to stay healthy?
"I'm pretty sure they sent me to you because of ecto levels in the city and the amount of fear I'd be able to consume naturally Uncle Jon." He states as he jams the needle into himself. Above him Bruce and Tim want to intervene but Cass stops them
"Not hurting him." She states. Danny shivers for a moment before shifting into a much more human form with black hair and blue eyes as they watch on.
"How human do I look?" Scarecrow grins widely
"You look great kiddo. How stable do you feel? What effects are there? How is it interacting with your biology?" Danny thinks for a moment
"I feel like I watched a horror movie in theatre and absorbed enough fear to last a few days." Scarecrow takes note of that.
"Eventually we'll find something that'll work more permanently." Crane vows
"How much fear do you need to eat weekly?" (The Bats listen closer if one of their rogues literally has to feed on fear that rewrites several prior assumptions about him)
"Not as much as you. I'm still mostly human and I tend to stock up on a bunch at once. I'm thinking about making a weak strain to inject myself with so I won't have to go out as much." His Nephew seemed surprised
"Really? Family tradition means that we need at least one Supervillain a generation and my parents have stopped doing vivisections in their basement so really it's just you?"
"Family tradition?" Tim questions but Bruce is almost as confused. He'll need to look into Jonathan Cranes background more after this if it's a family tradition. He's also concerned about the vivisections the boy mentioned.
Scarecrow let's out a bit of a laugh below them.
"Who will be the villain from your gen then?" He mused
"Any one of us really," Danny laughed "According to the Government I'm breaking the law by existing. Ellie is half raised by Uncle Vlad and he's enough of a villainous fruit loop, Dan is on probation for murder, and Jazz wants to be a psychologist." He explained.
"Jazz I'm sure." He smirks as the Bats take notes