The Tempest
Summer before senior year Danny gets really roughed up in a ghost fight. Ends up in ER with stitches to head, gashes in back and side, and more down back of left shoulder. Concussion, pretty good one, requires overnight stay. The concussion thing is done with Sam holding up fingers and asking how many, and Danny replying very quietly four. She only held two up. Then when he tries to sit up he groans and they realize he really is hurt. More so as the blood starts soaking through his hair and dripping down his neck, and then face when he pitches forward, dizzy.
But the blow either knocks sense into him, or the shyness out of him, because he quits letting himself get bullied and treated like crap at school. And Sam and Tucker, too. He stands up to people, takes them down verbally, and eventually physically when he finds Sam being harassed by a made up A-Lister. Dude is trying to get her to go out with him, and she's refusing, and he refuses to take no as an answer, so Danny jumps all over him, shoving him back and telling him to get away from her. Dude is all over Danny saying, "I was talking to her, not you," and Danny tells him that she said no, and there's a fight.
Make it that the initial change is noticeable, but not truly worrisome. And as the months wear on things get really noticeable, culminating with the night Danny pops into Sam's room as Phantom and she freaks at him because she's wearing a towel. He responds, "If I really wanted to see you undressed, you wouldn't be able to stop me." And then at her pale and frightened expression he'll just laugh and say he could poke his head through her wall, her ceiling. Not that he wants to force her. And then he'll shrug and say, "Besides, this isn't what I had in mind for seeing you like that." And she'll get startled and ask him what that's supposed to mean, and he'll ask her, "Do you want the truth, the real truth? Or a pretty made up lie?" She'll opt for truth and he'll stalk to her, backing her into a wall and caging her in with his arms in either side of her head as he leans close enough that a breath is all that separates their mouths. "Because the first time I see you naked, I want you to be writhing underneath me and screaming my name."
This drives Sam to calling Tucker, freaking out and upset, and they go see Clockwork, who explains that it will pass in time. It's a ghostly puberty thing, and Danny is sacrificing pieces of his humanity to stop himself from losing complete control over his powers as they grow and change. They wonder if he knows what's going on, or if that's a piece that is missing. Tucker gets to see exactly what happened, and then they get to see a current image of Danny floating above the city alone, above the clouds. He looks upset, really upset, and scared. They understand that he doesn't like this, he knows exactly what's going on, but that he can't change what's happening because he might hurt someone. To which Clockwork shows them some excerpts from his last battle, which ends in three ghost vultures being three steaming piles of ectoplasm. Nothing left over. Clockwork tells them it'll pass soon, and makes a passing comment that perhaps they should be careful of the games they play in the meantime.
So they try to go on with it, and toss in some escalating changes beyond that, beyond the fight at school. It's a really noticeable thing now.
He ends up getting caught out as Danny Phantom, not because he's standing up for himself and all, but because there's an accident and Danny saves Dash. He has no other choice, he can't let Dash die just to protect his secret identity. Maybe truth or dare before revealed. Maybe that's why Dash is in danger, he got dared something stupid and actually did it?
Before that though, Danny could have a really wicked grin as he asks Sam truth or dare, and she'll want out of the game because she just knows he's going to do something bad, no matter what she chooses. And he will. If she picks truth he's going to ask her how she really feels about him, and if she picks dare, he's going to dare her to kiss him.