Note: This is at least partially based on some ideas in my story, Symbiosis. Also thematically it is really similar to what I'm doing in Face to Face. Both stories would be about Fenton and Phantom realizing they need each other, subsequently accepting themselves as a halfa, and choosing to refuse/fuse. That similarity is the reason this most likely won't even be expanded beyond this but enjoy anyway.
The first thing the ghost remembers is the swirling green light of the ghost portal, metal walls of a lab, and a teenage girl and boy crying frantically over an unconscious boy in a white and black jumpsuit. That is until the boy on the floor blinks at his friends and sat up. While the three hug and cry, the ghost tries to get their attention, asking what's going on. But they can't see him. No one can. The ghost wanders around for a while but is drawn to the building he first appeared in and to the family, especially their son who apparently is called Danny Fenton. The name and the boy seem familiar but the ghost can't tell why.
Things change when the first ghosts show up out of the portal. The ectopus attacks one the Fentons' older neighbors and the currently unnamed ghost swoops in to stop it. He swiftly beats up the other ghost, sending it fleeing. Then he checks on the hiding older woman, who calls him a Phantom right before fainting. That's how the ghost gets his name, Phantom. Now Phantom thinks he knows why he's here. He protects Amity Park's humans by fighting the unruly ghosts that come through the portal. Though he doesn't fight all the ghosts. He becomes friends with a black and white ghost boy at Casper High called Sydney. The other ghost shows Phantom his lair in the ghost zone, eventually spurring Phantom to explore the GZ himself. Phantom eventually finds the Far Frozen and becomes friends with the ghosts there. Phantom splits his time between hanging out with his new friends in the GZ and hanging around Amity Park. He's happy overall, though still feeling like something is missing. He still doesn't remember who he was and doesn't know why he looks a lot like Danny Fenton. He's still drawn to Danny but is too scared to show himself to him; what if the boy tells his parents and Phantom gets captured.
And what Phantom fears happens. One day, he isn't careful enough and he gets captured by the Fentons. While Phantom is freaking out because the Fenton's are going to dissect him, Danny sits downstairs feeling very uncomfortable with his parents' excited talk of what they plan to do to their prize. Since the accident, he's also felt like something's off. He knows he almost died in the portal but it's something more than that. Plus, Danny's noticed his ghostly stalker, though he's not weary or scared like he expected. In fact, he's interested, fascinated even; Danny thought about approaching Phantom after a ghost fight at the school but he couldn't work up his courage. Now though with the ghost downstairs, he can't help but investigate.
He walks downstairs to find a crying Phantom and he's mesmerized. The ghost looks exactly like him…well not exactly. Like an inverse copy, a reflection. The boy instantly feels a connection, a kinship to the ghost and knows he had to help him. Danny helps Phantom escape by letting the ghost overshadow him, the only way for Phantom to get past the Fenton's ghost shield and alarm system.
Later- after a trip to the Nasty Burger because Phantom really wanted to try a milkshake, Phantom tries to stop overshadowing Danny but can't. The two are stuck together and everything they try including every Fenton invention that won't destroy Phantom, but nothing works. So they wait, trying to figure out what to do. To both boys' shock, they find that they can transform into a ghost and Danny can access Phantom's powers, even in ghost form.
And Phantom also discovers shocking things. Before overshadowing Danny, he hadn't remembered anything about who he was before he 'died.' But being in Fentonworks and around Danny's friends, he starts remembering. But in the memories, he looks like Danny Fenton. At first both of them think Phantom must just be seeing Fenton's memories but the ghost just knows that they're his somehow. And that doesn't explain why he felt drawn in Fentonworks before meeting Fenton or why he and Danny Fenton look so similar, even before fusing.
After trying everything they can think of, they go to Phantom's allies in the Far Frozen for help. Frostbite is understandably shocked when they transform into human form and the human Phantom is overshadowing looks almost exactly like Phantom. The yeti almost immediately realizes something, that Phantom is a very rare kind of ghost-he's an Echo of a still living person. Ghosts are formed by the emotions of a human's death; they aren't the actual soul of the human but are copies with varying degrees of accuracy and depth of personality. And Phantom is a very close, very in sync copy. The pair have very mixed reactions. This explains a lot of the connection between Phantom and Fenton. And Phantom knows who he is now, at least partially. But he doesn't feel like a real person, not that he's ever really felt real and confident in himself. Meanwhile, Fenton is shook, he hadn't really realized how serious his accident was. But knowing about this dead, ghostly version of himself can only be described as haunting.
But they still don't know why they're still stuck together. Frostbite promises to do some research. They can go back to Amity Park, back to ghost hunting and school and hanging out with Sam and Tucker. Back to figuring out how to live as a ghost and a human (who are almost the same person but not quite) sharing the same body. The two are starting to make peace with their situation and their identities. Until…..
Frostbite sends a message saying he has the answer for them. After the return to the Far Frozen, he tells them of an all legend and prophecy he found in an ancient book in the Far Frozen's library. It's the Legend of the Halfa, a being that is both a ghost and a human. After some research, Frostbite found out that the two cannot and should not be separated. They are becoming the Halfa but they aren't done yet. To the shock and mild horror of both of them, Frostbite explains that the Halfa isn't a ghost overshadowing a human or even a human and ghost living in symbiosis. The Halfa is one being, in body, soul,….and mind. The pair's minds will and have already begun converging, memories, thoughts, and emotions swirling together as the distinction between Phantom and Fenton blurs and disappears. It's a confusing, distressing, and at times painful process as the two minds fight to stay separate. Each wants to stay separate on some level but the pull, the draw is so strong. And they are so, so scared. Both are terrified of what Sam, Tucker, and Jazz will think, of what Mom and Dad would think if they knew. But the three teens who know about Phantom eventually get the pair to tell them what's happening. They're understandably upset but eventually accept it. Surprisingly, Jazz is the first to come around; she'd sensed that the human version of her brother hadn't been himself since the accident. So when the crying almost-half ghost comes to her for comfort, she accepts them with open arms. One voice-that's two-that's one ringing with pain, Phantom and Fenton pour their heart and core out about all the confusion that is their existence. Physically, their form is unstable, shifting. Black hair bleeding into white and white hair into black; blue eyes bleeding into green into blue in rapid succession. Mentally, they keep switching mid-sentence, even mid-thought. One Danny will speak and to his horror forget if he's the human or the ghost. Or is he both? Neither? The almost-half ghost keeps switching between we and me, they (he?) can't remember if he (they?) are one person or two. And both (?) are so scared of losing themselves, of who will they(he?) be when this is over. Jazz hugs the weeping figure, promising that no matter what they'll be her brother. They'll be Danny. And she loves them, she loves Danny no matter if he's human, ghost, or both at the same time. The word comforts the boy(s) who gratefully accepts the hug.
Finally, Fenton and Phantom fall asleep…. and Danny wakes up. Danny Fenton-Phantom, Danny the halfa, wakes up in his bed. And he (HE) is at peace. After all, Phantom wasn't ever supposed to diverge from Fenton. They…he was supposed to come out of the portal as the Halfa. Danny's finally the person he was supposed to be.