What if Agent O and K decided to play it smart?
They know that Doctors Fenton are extreme in their beliefs of ghosts, they silently fear them in their ideologies and theories of what they actually are. That saying "people fear what they don't understand". That's the Fenton parents.
However, becoming the ones that ultimately fund their projects, the Agents become more involved, cracking down on safety, providing that deceit of caring.
They know that there's something wrong with the kids, particularly the youngest. They know but they never bring it up, not to the kids, not to the parents, just silently watch from a distance and wait for an opportunity.
So when Danny finally tells his parents the truth, and it seems to go well, it's the Agents that find out by the Doctors' separate project file in an attempt to fix their son.
Finally, their patience pays off. Continuing their deceit, they allow the parents to go with the plan of vivisection. [Some of the agents not involved with the Fentons have a problem with the fact that Danny is still just a kid].
So Agents O and K rescue Danny from his own parents and continued to deceive him. Brainwashing him into believing that they care for his well-being.
They've been protecting him and helping him understand his own powers, get a better understanding of his biology.
His allies continue to tell Danny that he needs to be careful.
In response the GiW start limiting his access to them. Not outright, just increasing training or theres a problem with the portal that it had to be shut down.
He goes on a few missions to help other ghosts or undead, and those end up telling him they're victims. That's where the doubt begins, so he starts to catalog everything in his head to realize that they're setting him up to be a weapon.
They've known from the beginning or mostly known that their was something off about him and they were waiting for the opportunity.
So he tries to get out, but through all their help of him, he can't. He's stuck, and he has no one to turn to.
Another hero or so finds out about Danny. Maybe they hear speak about a potential weapon. Someone decides to go looking, maybe they end up as an internal informant to relay information to the others who are trying their hardest to get Danny free.
Danny has to put trust in strangers who say they'll help him, but it's better than becoming a weapon.
[If there are any fics like this, please rec them to me?]