AN: We are gonna do a time jump of about a month here. Why? Cause I want Danny to be healed enough to join the action! Don't worry, there will be some flashbacks and whatnot to fill in some blanks, but I want to get this thing moving, so here we go!

Oh wait . Gotta disclaim first, lol. I don't own Danny Phantom or Young Justice.

Superboy exited the bioship, feeling pleased with himself. Their mission had gone quite well, no unexpected explosions or insane metahumans. It had actually been a simple recon mission. He was a little disappointed he hadn't got the chance to punch someone, but overall, the lack of complications was a good thing.

"Superboy! How did it go? Is everyone okay?"

Superboy smiled. There was Danny, regular as clockwork. The halfa was always there when they returned from a mission, anxiously waiting confirmation that they were all still alive and in good health. It probably didn't help that the first time Danny met them, they were losing. Badly. They had tried to tell him that their battles didn't usually go like that, but he didn't seem convinced.

"Relax, man. We're all good."

Wally was suddenly there, an arm thrown around Danny's shoulder. Danny yelped, phasing out of the grip instinctively. With his support gone, Wally face planted.

A peal of laughter brought Superboy's attention back to the bioship, where Robin was descending.

"Well, we were all good. Pretty sure the Wall-man is no longer feeling the aster." the Boy Wonder said, still laughing.

Danny blinked, looking at Wally. "Ah! Sorry, I didn't mean to! Are you okay?"

"S'all good." Wally mumbled, still face first on the ground. He lifted his head a little, smirking. "My bad anyway."

Aqualad sighed as he left the ship. Danny looked at him nervously, trying to spot the girls still on the ship.

"They are unharmed Danny." Aqualad said kindly. "The mission went… unusually well."

Tension drained out of Danny, and he smiled slightly.

"Good. That's… um good. Yes." Danny fumbled a bit, rubbing the back of his neck as he blushed.

Robin and Wally exchanged amused looks before converging on the embarrassed halfa.

"Come on man." Robin said cheerfully. "I need to tell you about how my hacking skills were the sole reason this mission went well."

"Hey!" Wally protested. "Without my speed, you never would have…"

Their voices trailed off as they left the room. Megan came up to him, wrapping her arms around his neck.

"Look at you." she teased. "You're smiling."

"Am not." he muttered, but he couldn't quite wipe the soft smile off his face. Megan merely laughed, giving him a quick kiss on the cheek before walking off.

Superboy sighed. So he had a soft spot for Danny. They all did. There was just something incredibly endearing about the kid. It didn't help that he was around Danny all the time. Danny lived in the Cave with him and Megan, so it was like a 24 hour assault of cuteness. Not even he could hold out against that.

Danny living in the cave was both a blessing and a curse. A blessing because he genuinely liked having him around, and a curse because of why he was there. When they had asked about his family, Danny had gone very still, before saying he didn't have any. They'd never asked again, not wanting to stress their newest member. With no other options, Danny had moved into the Cave.

Connor snorted mentally. 'Moved in' implies that he had something to bring over. Danny hadn't had anything, just the clothes on his back, and a pile emotional problems.

Though really, there were fewer of those than there should be. Sure, Danny reacted poorly to unexpected touch, he got anxious easily, and Connor knew for a fact that he had nightmares fairly regularly. But besides that, and a few other little oddities, Danny functioned remarkably well. Heck, he had adjusted better than Connor had himself when he had been rescued from Cadmus.

He'd asked Danny about that once. The halfa was the only other person on the team who really knew what it was like, to be an experiment in a lab. He'd wondered how Danny dealt with it so well.

"It's just pain." Danny said. "I'm used to that. Sure, it sucked, but it's over now. No point whining about it."

"But it's not just the pain," Superboy argued. "Doesn't it bother you, how they treat you like you're not human, like you're lower than them?"

Danny looked at him blankly.

"People treated me like that long before I was captured."

Connor frowned, remembering that conversation. That had been an uncomfortable look into Danny's life, and he had immediately changed the subject, unwilling to deal with the complicated emotions it called up. He was slightly ashamed of his reaction, but he got the feeling that Danny didn't want to talk about it either, so he tried not to let it bother him.

Superboy shook his head, annoyed at his own train of thought, and headed toward the kitchen. Odds were that would be where the rest of the team was. A quick check with his advanced hearing confirmed his suspicion.

Robin and Wally were still arguing when he entered the kitchen. The only difference now was that Artemis had joined in, saying that they were both useless and that she had been the real mvp. Megan fluttered around the arguing teens, trying to keep the peace, while Aqualad just watched with a long suffering expression on his face. Danny stood alone, looking more and more bewildered as the argument continued.

Suddenly, they all fell quiet and turned, looking at Danny expectantly.

"Well?" Artemis asked crossly. Danny's mouth opened and closed a few times. He looked completely lost.

Superboy winced. He knew how Danny was feeling. Danny's hearing was better than a normal human's. Not quite at his level, but still advanced enough that multiple people screaming at once would have been extremely confusing, borderline painful, to him. Connor knew from experience how hard it was to filter out the layers of sound that built up in places like the kitchen, where the hum of appliances could be very distracting. It didn't help that yelling reminded Danny of his time in the lab.

Superboy was about to step in when Danny spotted him. Relief spread across his face.

"Superboy!" he yelled, a strained smile on his face. Connor could hear the plea for help in his voice.

"Superboy? He didn't even do anything! How could you say that he was the most useful member?" Wally yelled.

Danny flinched at the noise, and Superboy could tell the situation was getting out of hand, fast.

"Hey Danny, wanna spare? I didn't get to punch anything on this mission, so I could use a good workout."

"Yes!" Danny yelped, running up to Superboy's side. "I would love to spar. Let's do it right now."

Danny fled the room, heading to the sparring pad. Connor waited until he was out of ear shot before glaring at his teammates.

"What on earth made you think that yelling was a good idea?" he hissed. "I've told you how upsetting that is to people with enhanced hearing. And that's without the… other thing."

The three who had been yelling had the good grace to look ashamed. Robin opened his mouth, presumably to apologize, but Connor cut him off.

"I don't want to hear it. Just… think in the future. Okay?"

With that, he turned on his heel and stalked out of the kitchen.

Danny was waiting for him in the main training room. Superboy felt some of his anger fade when he saw him. Danny was shifting his weight back and forth, looking all the world like an excited little kid.

Contrary to what one might think, Danny loved sparing. They had been nervous when Danny had first asked to train with them.

"Are you sure Danny?" Black Canary looked concerned. "You don't have to do this. We don't want you to feel pressured into anything you aren't comfortable with."

"I'm sure!" Danny insisted. "I want to learn how to defend myself. I need- I need control. I want to help people, and I'll never be able to if I don't learn how to use my abilities properly!"

Black Canary looked at him consideringly.

"Alright." she finally said. "We'll start slow, see where you're at and go from there."

Danny's grin was blinding. "Thank you!"

Danny had improved leaps and bounds since that day. His range when it came to types of powers was impressive, and he was learning to actually use them to their full advantage. When he had started working with Black Canary, it had been obvious that he had quite a bit of fighting experience, but no formal training. Under Canary's tutelage, he had become a force to be reckoned with.

Personally, Superboy thought Danny was ready to go into the field. Robin had said that Batman was waiting for Danny to be in a 'better frame of mind.' Superboy was pretty sure that leaving Danny behind to fret was worse for his frame of mind than putting him in a combat situation would be, but no one asked his opinion. In the meantime, he would just do his best to make sure that Danny was prepared to fight to the best of his abilities when the time came.

"Ready?" Danny asked with a grin.

"Hit me with your best shot." Connor shot back with his own smirk. And they began.

Danny and Connor spared for almost an hour. Neither of them were really giving it their best; they were just blowing off steam. They finally stopped, exhausted from fighting almost non-stop for so long.

Danny flopped on the ground, breathing heavily. Connor squatted down next to him, amused.

"Tired?" he asked with a smirk. Danny squinted up at him.

"I hate you." he muttered. Connor laughed, sitting down all the way.

"Chill, I'm tired too. I don't usually go that long."

Danny hmm in agreement before lapsing into silence. Connor didn't mind. Danny didn't tend to talk much. He could understand that. Connor didn't like to talk much either.

They lay in companionable silence until it was broken by Kid Flash racing into the room.

"Guys! Guess what! The League is coming here! Like, all of them!"

"What? Why are they coming?" Danny jerked up, staring at Wally in alarm.

"To meet you dude!" Robin crowed, entering the room with the rest of the team. "They want to meet our new member."

Danny did not look happy about that. He hadn't met very many leaguers. He mostly interacted with Black Canary and Red Tornado. He had met Batman a few times, but that was it. Meeting a large number of new heroes at once must have seemed incredibly intimidating to the shy halfa.

Superboy was also upset, but for different reasons. If the League was coming, that meant that Superman would soon be here. Connor hated being around Superman. The man was just so awkward and uncomfortable around him. It made him feel worthless, like he could never be good enough to bear the Super title.

"Superboy? You don't seem very happy. Aren't you excited to see your dad?"

It took Superboy a moment to register Danny's voice. When he did, rage fell over him. Without thinking, he screamed at the shocked Danny.

"Shut up! You don't know what you're talking about. Superman is not my father!"

He stormed out of the room. He vaguely registered the others explaining things to Danny, but he didn't listen. He needed to cool off before the League arrived.

Already he felt bad. Danny's scared face kept flashing in his mind's eye. He felt sick. How could he do that to Danny? It wasn't his fault that Superman refused to acknowledge him. And it wasn't like anyone told him his true connection to Superman.

Superboy huffed. He needed to get over himself. Superman would never welcome him into his life. He needed to accept that and move on.

Connor ended up on a ledge overlooking the ocean. He had found this spot early on in his stay at the Cave, and it had always had a calming effect on him. The best part was that no one else knew where it was, so he could stew undisturbed.

"Connor?"

Superboy nearly groaned at the sound of Danny's voice, but he stopped himself just in time. He had no clue how how the halfa had found him, but now that he was here, they might as well talk. He gestured at the ground next to him, and Danny sat down gingerly.

There was an awkward silence until Danny broke it.

"I'm sorry. I didn't mean to upset you."

Superboy sighed. "It's alright. I overreacted."

Danny shifted nervously. "So… you're Superman's clone?"

"Got a problem with that?" Connor snarled.

"No!" Danny exclaimed, looking genuinely hurt that his friend would think that. "It doesn't matter how you were made. You're still a person."

Superboy slumped, shame creeping through him. "I'm sorry. It's just… Superman is a sore subject with me."

"Why?" Danny asked, confused.

Superboy stared at the ocean, unwilling to speak of such personal matters while looking at Danny.

"I just wish he would acknowledge me, you know? I mean, I have a pretty good grip on my abilities now, but I could have used his help in the beginning. And he's the closest thing I do have to a father, so it hurts that he just ignores me."

Danny stared at Superboy with wide eyes.

"Wait." he said slowly. "You're telling me that you are a clone of Superman, and he completely ignores you? Never helps, doesn't reach out at all?"

"Well, yeah." Connor said.

Danny had an interesting look on his face. Superboy wasn't quite sure what the expression meant. He had never seen Danny look like that.

Distantly, he heard the zeta tube go off.

"They're here." he said with a sigh, bracing himself to face Superman.

"Oh really?"

Superboy startled at Danny's voice. He had never heard the halfa speak in a voice spitting so much venom. Danny got to his feet and sank through the ground, heading toward the main hanger. Right before he disappeared, Superboy finally recognized the look on Danny's face.

It was rage.

Worried all of a sudden, Connor ran to the main hangar where all the heroes were congregating. He arrived just in time to see Danny puch Superman in the face.

Superboy watched in awe as the Man of Steel staggered back a step. Danny must be incredibly angry to put that kind of force behind a punch. Superman straightened up, looking at Danny in shock. He began to speak, but Danny interrupted him.

"How dare you!" Every inch of Danny radiated righteous anger. "How dare you neglect your child!"

Superboy's eyes widened. This was about him?

Superman seemed equally shocked. "I don't know what you are talking about. I don't have a child."

"Yes you do!" Danny screamed. "He's standing right there!"

Superboy jumped as everyone in the room turned to stare at him. He felt extremely uncomfortable under the scrutiny.

"Danny, it's okay." he placated, desperate for the confrontation to be over. He did not really want this kind of attention. Danny merely turned his glare on Superboy.

"No it isn't. He has a responsibility toward you, and he should not get away with neglecting it!"

"How is he my responsibility?" Superman argued. "I had no hand in creating him."

"So?" Danny said bluntly. "Lots of parents have kids unexpectedly. Doesn't mean they are allowed to completely ignore them."

Superman shook his head, looking frustrated. "You don't understand." he dismissed.

Danny's face darkened even furthur.

"Oh really? I don't know what it's like for someone to use me against my will in an attempt to create a weapon? Hm? Is that what you're saying?"

Superman looked understandably uncomfortable at that. Everyone in the room was quite aware of Danny's… unfortunate past.

"It's not the same." he said weakly.

"You're right." Danny spat. "It's different because none of my clones survived."

Dead silence fell in the room. Superboy's mind went completely blank. His clones?

"They wanted to recreate me." Danny said bitterly, filling the silence. "They were obsessed with figuring out how it was possible for a creature like me to exist, stuck between the dead and the living. They tried to recreate the accident that made me, but it never worked. All of their test subjects died, because apparently, I'm one in a million!"

Danny's voice took on a faux cheery tone at the end, sounding a little more hysterical than Superboy was comfortable with.

"They finally gave up on that and moved on to cloning attempts. Unfortunately, I'm extremely difficult to clone because of my shifting DNA."

Danny took a deep breath, his voice suddenly shaky.

"Do you know what it's like?" he whispered. "To be tortured as people try to extract your very essence so they can replace you? Only for it fail, repeatedly? To be forced to watch versions of yourself dissolve into nothing? To watch as they are cut apart, and melted down, and destroyed in every way imaginable, just to obtain one data point? To hear their screams and know that you can do nothing for them? I had to watch them die, over and over and over."

Superman stared at Danny in undisguised horror. Danny didn't notice, lost in memories.

"There was one…" he mumbled, placing a hand on his chest. "One that was more stable. I would have done anything for her. But in the end…"

Danny shook his head, scrubbing at tears that were filling his eyes. He glared at Superman, his fury returning.

"You're lonely right? Only one of your kind? Last Son of Krypton and all that? Well guess what? Your not alone anymore! There is a perfectly good kryptonian right there. He is here, and stable, and alive, and you are throwing him away like he is nothing!"

Superman had nothing to say in response to Danny's accusations. He looked away, unable to keep the furious boy's eye. Danny snorted disdainfully.

"You are not the man I hoped you would be." he said. Without another word, he stormed out of the room. He left silence in his wake.

Superman looked around, but no one was willing to meet his gaze. He met Connor's gaze, and for a moment the clone thought he might speak to him. Instead, Superman turned around and entered the Zeta tube, leaving the Cave. His authorization code rang loudly in the silent room.

After a long moment, Robin cleared his throat awkwardly, glancing at his guardian.

"Well, that was… something. What do you think Bats?"

Batman stared at the doorway the halfa had disappeared through, deep in thought. Finally, he turned back to his ward.

"I think," Batman said, with an oddly satisfied air to him, "that Danny is finally ready to enter the field."

AN: Hmm… Theory: The reason Danny and Vlad survived their respective accidents was because they both had prolonged exposure to ectoplasm over time, Vlad through his research, Danny through living in the Fenton household. Also explains why Vlad had a poor reaction at first and Danny didn't. Danny had more exposure, especially while developing. Thoughts?

Also, confession time. I'm a little embarrassed, but here we go. I didn't really think about where this was going to fall timeline wise when I started it. I just used the characters I wanted. Now, when I think about it, it makes most sense for this to be sometime in the gap between seasons 1 and 2 of Young Justice.

You may see a problem with that.

That's right. No Zatana or Rocket. I just don't know those characters as well, so I didn't want to write with them. Soooo…. For the sake of this story, we will say they just… showed up later? That cool? Sorry if you're a huge Rocket or Zatana fan. Just know, I would not have done them justice. :/

ANyway…. Bye? (Again, sorry for excluding two killer female heros. I am so ashamed.)

(PS. I can't remember if Superboy and Superman reconciled by the end of season one. If they did, ignore it! Imma twist the cannon to make this story they way I want, and no one can stop me! Hahahahahahah!)