Ok, now cross this with Danny being the Bio kid of Dick.
Someone tried to clone him, but they couldn't quite figure out the technology. The closest they came was a test tube baby (like Talia does to Bruce to make Damian). Now, this villain might be a Bad Guy, but he realises that this is a life he created, albeit unknowingly. So they let the incubation last until Baby Boy is born, then get a goon to travel to the other side of the country and drop him off at a hospital anonymously.
They wash their hands of the whole failed cloning affair and turn to their next attempt to bring down Batman: figuring out his identity.
Cut to 15 years later, and Danny getting caught by Batman as he tries to capture Johnny.
He is already looking into the Amity Park situation since Clark called him in a panic 4 days ago, saying that a ghost kissed him in front of Lois, so Johnny calling this Meta Phantom helps him narrow down his search. The photos of the ghosts may glitch, but now that he's seen the boys face in person, he recognises that he's identical to the son of mad scientists Jack and Maddie Fenton. He was already looking into the boys birth due to his starting resemblance to Dick - it would be a lovely surprise to both boys to find out they had more family in the world - but now that he'd accidentally outed Jaylad's identity, his search became much more urgent.
(In this au, the GIW are actually a privately funded paramilitary organisation that is operating illegally in the United States. They know enough legalese jargon to fake some laws being put into place so that the local civilians won't put in calls for help or put up any form of resistance)
Bruce calls in a favour from Barry, who some over there during his lunch break to grab some hair from the boy's pillow while he's at school, and he is able to start a DNA search to see how distantly Danny and Dick are related. Since the Bad Guy from before was so bad at his job, there's no generic markers for cloning, and the test results showed that Dick somehow fathered Danny when he was 12 years old. Que Bruce freaking out before looking at the 'Mother's' DNA, only to find that it belongs to that D grade villain that was a nuisance for about 6 months before accidentally killing himself in a lab accident.
Several sleepless nights later, and he tracks down the reformed former goon, who now works as a Mall security guard in Ohio. The man had almost forgotten the whole affair but remembered enough to fill in the blanks in the storyline Bruce had put together.
Almost two weeks after Danny first showed up in Gotham, Bruce had a complete write-up of Danny's life - from conception to when he developed his powers. The technology started glitching around that time, so it's hard to gather an accurate recounting of events.
Dick has come to town for the weekend, and he starts to make a joke about how 'B better not Full Name me while I'm out there tonight', but stops when he sees the look on his dad's face. That's the 'I have news and you're not going to like it' face. "What happened? Did he go to the press?"
Bruce hands over the file. Attached to the cover is Danny's most recent school photo, and at first glance Dick thought it was of him. "I found the identity of the meta who goes by the name Phantom. His adopted name is Danny Fenton, but biologically, he's a Grayson."
As Dick collapses into the couch in shock, he's glad that B cleared out the area before starting his explanation.
"I've got a compilation of photos in there, combined with anecdotes attached, for if you wish to learn about the life he's led so far. There's a separate file in the Cave with all the details behind his birth if you want to go over it later. I understand this is a shock. I'll stand by whatever decision you make going forward."
Dick stares down at the picture of Danny. Of his Son. He reaches a hand forward to run his fingers over the photo before handing the file back to Bruce. Anything he needs to learn about Danny, his son can tell him in person. Looking up, he sees that B already knows his decision.
"Alfred has the civilian jet prepared and ready to go. All you have to do is decide who you want to come with you."
Meanwhile, in Amity Park, Danny is finally starting to relax. It's been weeks, and there's been no word from Batman or any of his boyband members.
He needs to hurry over to Tucker's house, his friend just called saying he found something important when he was going through the GIW files they stole yesterday. If he's lucky, Mrs. Foley will invite him to stay for dinner.
