The clone does not destabilize in the end, despite being sure that he would. Exhausted, he turns human and is powerless because of the chip. The chip electrocutes him as he tries to transform again. He should help D... the boy fight Vlad. But he hits his head so he passes out and stops breathing. After capturing Vlad in the thermos, Danny goes to check on him and gives him CPR. He's very relieved when his clone's heart restarts.
Danny takes the other boy upstairs, finds his room, and treats his injuries. He puts the clone in his bed and goes off to figure out what's happening. He finds the packed supplies and the notebook down in the lab. He flies back up to the mansion and is flipping through the pages when he hears a clatter in the bedroom and then the sound of throwing up.
He phases into the bedroom to find his clone heaving over the toilet and the bandages on his head red tinted. Danny tries to talk to the other boy. There's angry yelling and denial. (You're not real. This isn't happening. This isn't real.) The clone ends up throwing stuff at Danny and yelling at him until he puts his hands up and walks away.
Danny's very annoyed now, after that reaction. He's fuming and angry himself. He finds the kitchen and realizes he's hungry. Danny starts boiling water for mac and cheese. While he's waiting, he looks at the notebook and…. he immediately feels bad, realizing what that reaction was. Part of him is disgusted and disturbed by the clone things he was the real Danny. But another part of Danny feels pity; the poor kid just found out everything he thought about himself was a lie.
Danny's still standing and reading when he hears the sound of the kitchen door opening. He looks up and he and the other boy meet eyes. A look of shock and fear crosses his face and the clone bolts. Danny runs after him. He ends up cornering the clone, who's trying and failing to activate his powers, in the hallway. The clone sinks to the floor, backed up against the wall.
"It wasn't….that wasn't a dream. I'm really… I'm really a cl-. I'm…I'm not real. I'm not real." He's crying. "No. It has to be a dream. This isn't real. It's not happening."
The other boy is spiraling, becoming more and more distraught and unfocused. Danny grabs his hand and… "You feel that? Your hand in mine. That's real. You're real. I'm real. We're both real. And we're here together."
"I'm not…I'm not real."
"Yes, you are." Danny squeezes the hand, reassuring. "You're okay. You're safe now. Just breathe with me, okay?"
Danny manages to talk his clone down until the other boy is coherent and relatively calm. He pulls the other boy to his feet and offers him some of the food he just made. The clone accepts cautiously.
The two talk in the kitchen. It's a very somber conversation, figuring out exactly what's happened, that the clone isn't the real Danny, the boy he'd woken up earlier was. The clone isn't in denial. He understands the truth but he's very clearly unhappy. He's grumpy and barely able to look at Danny.
There's a debate about what to do now. The clone tries to just leave but he's powerless and the chip shocks him if he tries to use his powers. Danny argues with him to stop and the clone insists they get the chip out.
The two go back down to the lab. They try everything they can think of to remove the chip but Danny can't even pull it out with his intangibility. The clone is ready to give up, feeling hopeless. And then Danny gets the idea that his parents might be able to get the chip out. There's another argument.
"Are you crazy?! How are we supposed to explain me" The clone motions to himself. "to Mom and Dad? They don't know about me…us…I mean you being Phantom!"
Danny insists they'd understand. And the other boy not getting hurt every time he tries to use his own powers would be worth it.
Eventually, the clone is convinced. He leaves with Danny, taking the car he'd picked out earlier. They're planning to go to Jazz's college where she's doing a summer program she can help explain. Cue the start of a sibling bonding road trip.
It starts out tensely. Danny and the still unnamed clone don't talk much. Both are clearly uncomfortable but Danny is trying to be nice. They go to a dinner for food and the clone tries a burger and a milkshake for the first time which actually makes him smile for the first time in front of Danny. The waitress thinks they're identical twins, which leads to a conversation later in the car about how that's technically true.
The clone warms up a little after that. He points out interesting sights and attractions as they pass them. He takes over navigating with the map they got at the rest area. Soon it's night and the clone falls asleep in his chair.
Later, he wakes up as the flashing of police lights. They're in the middle of nowhere. Danny's whipping around corners and looking for a way to get away. He pulls off, hiding between some trees. He turns the whole car invisible and they wait for the police to pass. The sirens disappear but…
"We need to ditch this car." Danny insists.
His clone agrees. With Danny being the only one with powers, he has to carry his counterpart which is awkward. They stop to rest in an abandoned building and get some sleep.
Both boys end up at Jazz's school the next morning. With no phone and not knowing where she is, both teens end up asking around for the red-head. Jazz is worried and a little annoyed. She finds the clone first and hurriedly shoves him into her dorm room. Danny pops into visibility and the pair have to explain.
The clone goes to the restroom and Danny reassures his sister that the other teen's a good guy. He ends up mentioning the 'having Danny's memories' thing which the clone isn't really happy about.
Continued sibling road trip! But with Jazz bonding and reassuring the clone that he's a real person and can be his own person. She encourages him to pick out his own name and he goes with Jamie, from Danny's middle name.
They end up in Amity Park. Danny tells his parents about his powers and about his clone. With the successful reveal, he goes out to the car to get Jamie. The other boy is unsure and awkward at seeing Jack and Maddie. But Maddie smiles at him, calling him sweetie. Jack gives him a bear hug. Jamie finally breaks down crying, calling them Mom and Dad.
So yes, Jack and Maddie agree to help their new son. There's a lot of angst, dealing with being powerless, with being a clone with fake memories. But Danny and Jazz are good siblings and help Jamie find himself. The Fenton parents learn about Danielle and adopt her into the family. And eventually Jack and Maddie manage to remove the inhibitors so Jamie can finally fly again.