Since the ending of the story was so confusing, hopefully Tucker can help clear things up for you a bit. Here's a little extra bit for you, and for convenience, we'll call it an epilogue:
Danny would later learn he was the only one who perceived the warping of time, a stretch, almost, as if Clockwork had not properly frozen things, but rather slowed it down. Sam and Tucker moved as if through molasses. Phantom and Plasmius both snapped out of existence, and then, with a roar, a black hole descended on him.
When he woke up, he was laying on his bed. He felt oddly depressed, and at the same time, relieved.
"Danny? You awake?" Tucker asked, looking up from his PDA.
The wave of affection Danny felt for his best friend was all out of proportion, but it didn't stop Danny from sitting up sharply. "Tucker!"
"What? Is something on my face?" the bewildered boy patted his cheeks.
"I … I'm just so glad to see you," Danny said. He blinked. "I don't know why."
"Well, I'm glad to see you awake," Sam remarked from the doorway, walking in, and Danny felt another rush of happiness. "Your sister's gonna get home soon. We did what we could with you, but if your ghost healing doesn't kick in and—oomph!" She coughed as Danny threw his arms around her waist, hugging her from the bed. "What?"
"Danny's happy to see us. He doesn't know why," Tucker explained. He rolled his eyes.
Danny sat back on the bed, letting out a little pleased breath. "What Tucker said. I'm glad Phantom didn't hurt you." He hesitated. "Wait. What happened there at the end? I remember Phantom kind of … I dunno .. having …?"
"Death throes?" Tucker interrupted. "Yeah. Well, I've done a little research—"
"By which he means 'read through Danny's Spider-Man Clone Wars comic books'," Sam interjected smoothly.
Tucker glared at her. "—And the best I can figure is something happened in the alternate universe that disrupted Phantom's existence."
Danny blinked. "Okay, so why do I still remember fighting him? Shouldn't everything be totally different now, since Phantom never existed?"
"Not necessarily. Because even though he ceased to exist in his own universe, everything he did in our universe still happened, since it's not the same universe," Tucker explained. "Comic book physics. You should pay more attention to your collection, Danny."
"Thanks for the advice, Tuck, I'll keep that in mind," Danny snorted. "Although, the explanation helps. Sort of."
"Glad to be of service," Tucker answered proudly. "You owe me a smoothie for the trouble."
"For reading my comic books?" Danny rolled his eyes, crossing his arms. "But … I'll buy you one anyway. And you too, Sam."
"What's the occasion?" Sam asked, raising an eyebrow. "Other than, you know, surviving your evil alter ego? Again!"
"Nothing." Danny shrugged. "Just … I feel like I've been missing you guys for ages." He shook his head slightly. "And while I really could just go for continuing my nap right now, I think I could really go for a smoothie tomorrow."
"You're acting a little weird, Danny," Sam confessed.
Danny nodded. "I know. I can't help it, though." He met her eyes.
"Huh," she said quietly, breaking her gaze away.
What Sam didn't say, and never did say, even when Danny went back to his normal, not-clingy self, was that she saw Phantom in his eyes.
He wouldn't understand.
Clockwork, however, might have.
Thank you again to everyone who read and reviewed this story! It was truely a pleasure to write. I look forward to seeing all of you around