TL;DR

Cheat sheet / Update schedule: I'm going to update this every week until my eight chapter buffer ends. While I have that buffer, I'm going to be working on writing a Master Challenge chapter, then a Phandom Phable, then a chapter for Pondus Omnium. Always look at my profile for update plans n such.

Please refrain from asking about chapters for any of my stories in reviews. You can PM me if your curious about how far along I am, but be kind. Stressing me out won't help. I will delete Guest reviews that ask about updates just so that my review count doesn't climb from them, seems unfair, nothing against the reviewer.


ABOUT ME HAVING A THIRD STORY UP:

Well, I thought I could avoid this, that I had greater self-control. But I can't. I have just way too many story ideas I want to write out. So I'm going to have to break my one to two stories at the same time rule. I just kinda came to the realization that I want to at least write as many of my stories as I can before they become irrelevant or end up rotting in my files. I wanted to wait until after I was done with Pondus Omnium and Master Challenge, but I want to write this. I need to know if I'm going in a good direction with this or not. I've honestly rewritten the start of this crossover six or seven different ways over the last year or so. Think in the vein of TheWhiteTitan in regards to multiple stories, although I don't think I'll ever publish as many stories simultaneously like they have.

Short version : I'm going to be publishing three stories at the same time (Master Challenge, Pondus Omnium, Young Justice Beyond). I have eight chapters of this done. I will be uploading them once a week until I run out. In the meantime, I'm going to be trying to write the next chapter of Master Challenge. I will be continuing my other stories. I fully intend to finish them (I have the endings and everything planned out and written in some cases). Always look at my profile for update plans n such.

Alright, onwards to the AN for the story.(This will probably be the longest you'll see in this story, I shouldn't need to do it again)


AUTHOR'S NOTE FOR YJB:

Well hello there everyone. Some of you have been waiting forever for this. Your reward has finally come.

This is just an AN here to explain a few things before the story begins. Just in case you wanted some background info before committing to reading.

Danny will be sixteen during the events of the first season.

Danny gains his powers in January of 2008. I tend to make Danny's birthday be in January too, so he turns fourteen about the same time, roughly. October of that year is when the episode Fright Night happens. Lucky in Love happens the March after that in 2009. He turns fifteen by that point. Then the Fright Before Christmas is that December. April of 2010 is when Danielle is made and Kindred Spirits happens. May is when Double Cross my Heart occurs.

Some of Danny's final episodes will be AU, starting with Reality Trip. Some episodes might not happen or be severely AU as well (be turned into longer story lines), so be aware of that.

The story will mostly follow the Young Justice Plot-line (cartoon and maybe a little sprinkling of the spin-off comics), though there will be original content along the way as well (AU Danny episodes as well as other things that you'll see eventually). This story will contain Season 1 and 2 of YJ along with extra parts and an original 3rd Season.

I'm also newish to the DC world outside of Young Justice and some other animated media, so have patience with me. I've been trying to practice these characters, but we'll see.

This Young Justice will be a bit AU as well because I will be altering a few things and of course adding things. This includes a larger recruiting rate for the League eventually (think Justice League Unlimited) and more for the Team as well. (I'll be careful about going too over board though)

I kind already have a set plan for who will be joining after the first season, but if there's someone you'd like to see (no OCs please) then tell me and I'll consider it.

Also this story is slightly Danny-centric but I'm going to try to have some focus on other characters as well, because they need love too.

Cannon pairings are in here and extra ones are already mostly decided. If you're dying to know what they are, PM me or review (I guess in the case of guests).

I think that's it…

Anywho, I hope you enjoy my attempt at this!


"C'mon, guys. You didn't think it was always going to be as easy as shoving the Box Ghost into the Fenton Thermos, did you? I'll be back." ~ Danny Fenton; Reign Storm.


Indianapolis. May 10, 2010. 18:36 CDT.

The TV had a news report on. It showed Icon and Rocket, two of the newer vigilantes to arise, talking to the reporter on site of a resolved robbery. White foggy steam rose from a cup of foamy coffee, and the light from outside of the apartment streamed through the divided window and lit up the white suit that was laying on a nearby dresser.

A brown hand reached out, with the remote. The channel was changed and displayed a different news report. "We haven't received much information, but we're expecting a press conference date to be announced soon. This is after the attack at the Amity Park Observatory, that resulted in the near death of five people and injury of two. It was supposedly perpetrated by two government agents that were trying to hunt a purportedly powerful ghost, level seven in caliber-"

The man who sat in a worn chair watching the broadcast, growled and clutched the remote. In one swift movement, he turned the TV off and chucked the remote at the screen. He saw it strike the screen and then clatter against the ground and grumbled.

Knock. Knock.

The owner of the small apartment glanced over at the entranceway, wondering who could possibly be visiting. The man stood and stalked towards the door and opened it.

"Hello, Agent Alpha."

Alpha felt his brows raise in surprise when he was presented with none other than the famous businessman Lex Luthor and his assistant. "Lex Luthor?"

"Ah, yes. That would be me." Luthor replied calmly and put one of his hands in a pants pocket. An easy smile came to the man's face that betrayed a kind of confidence that belonged to a king, secure and knowing of how far his name could get him.

He was utterly baffled as to why the businessman would visit him. Alpha frowned. "Why are you here?"

Luthor nodded towards the inside of the apartment. Alpha stood for a moment as though he was suspicious of how Luthor knew how to find him. Ultimately he seemed to make his choice and turned slightly to let the man inside. He watched Luthor's female assistant follow, before shutting the door and coming to sit down with them both.

"I suppose I'll start by asking how things have been since you were shut down by the government?" Luthor asked aloofly. He crossed his leg over the other and let three of the knuckles from one of his hands support his chin and jaw.

Alpha narrowed his eyes and gritted his teeth. "How did you-" It was a stupid question really, but he was insulted by the subtle play to throw salt on an obviously open wound.

"I'd imagine it's fairly easy to figure out that there would be a lot of people let go in the department, no? You were the head of the division and as such you are responsible for the actions of your men, no matter how foolish, unfortunately." Luthor interrupted and lifted one brow. Alpha leaned back in submission.

"What does a businessman like you want with someone like me?" Alpha asked plainly, ready to stop playing games to get to the bigger picture. Luthor smiled at the man's body-language thus far; he'd made yet another good choice.

"I feel as though the government is making a big mistake. Ghosts, as we've seen in the last year or so, are very dangerous. There needs to be people like you there to capture and take care of them…" Luthor trailed off before his face darkened due to a shift in his expression. "By whatever means, necessary."

Alpha didn't notice, but Mercy was preparing her gun. "Are you wanting to hire a private group to hunt ghosts?"

Luthor hummed, his more friendly demeanor returning like it hadn't left. "Something like that."

"How do you expect to get ahold of the technology we'd need to hunt them?" Alpha questioned.

Luthor smirked. "I'm sure you and I can come up with something for the time being. Wouldn't you agree? You've got to have a few things hidden away, possibly some contacts..." He gestured towards Alpha as his finished and waited for the man's response.

Alpha grew quiet for a moment before he spoke again. "Why do you even want a private ghost hunting team?"

Luthor stood up from his seat and stared down at the ex-agent, which was something most people couldn't manage when Alpha was standing, seeing as he was a large man. "You believe ghosts are a danger to humans, correct?"

"Yes, of course. They're more powerful than us, faster than us, can do things no mortal can, and they can sway hearts much too easily. They're deceptive and vile creatures."

"I offer you this. I'll fund your people. I know a good deal of your group was fired or arrested and a very few remain with the government, but whoever you can still gather together will do."

Alpha sat in thought for a moment. "You'd fund us, just like that?"

"You'd be surprised at what I'm willing to do for the good of the people, Alpha." The smile on Luthor's face looked benevolent by all outward appearances and just like that a spark of understanding seemed to register in Alpha's mind.

The former agent stood up, towering over Luthor as he gave his answer. "Very well. I'll join up with your private group. You're right, the government has made a poor mistake." He reached out a hand to meet Luthor's and they shook on it. Alpha had a feeling that this was the opportunity he needed to make the word a better place.

"Excellent. I'm very happy you'll be joining us." Luthor then broke off the hand-shake before walking towards the door. Mercy followed obediently behind him after returning her weapon to the standby position, secretly. "We'll contact you when we're ready let you see where you will be working."

"Yes sir. Do you have any requirements or suggestions about how we should operate? I just wanted to be sure I knew what you were hoping for."

Luthor paused and smiled at the door. He then turned his head slightly and looked over his shoulder. "There will be a bit more subtly this time around if you don't mind. I have some people that can help show you what I'll be expecting of you."

"Understood."

Outskirts of Amity Park. May 16, 2010. 20:55 CDT.

Danny Phantom, the white-haired green-eyed self-proclaimed protector of Amity Park, Indiana, sighed as he leaned up and looked around. After not seeing the beast nearby, he glanced down at himself. Stretching from his shoulder to his upper chest were three long claw marks. He hissed in pain as he watched some ectoplasm well up there; he also took note of the frayed edges of his torn hazmat suit. "Dumb giant blue lion. Why can't he just hold still?"

Carefully, Danny floated up into the air and looked around, trying to figure out where the ghostly animal had run off too so they could start round two. It wasn't a super dangerous ghost, but some of the people in Amity Park had been worried that it would try and eat their pets or something, so Danny had gone out to take care of it. "Maybe having Sam and Tucker here wouldn't have been a bad idea." There was an end of the school-year exam tomorrow and Danny had insisted that his friends didn't come with him for patrol this time. He had studied a passable amount and had figured he would head home after catching the lion. At least that way his parents would think he made it home for curfew and he could pop back out, in the event more ghosts decided to show up.

Danny glanced down at his shoulder again and smiled when he noticed the cuts had already healed up and it was as though he'd never gotten hurt. "Thank you, healing factor." He focused a bit more and his hazmat suit slowly knitted itself back together. The half-ghost then continued his search of the forest-line for the blue lion. In the middle of slowly rotating in the air and using his night-vision to look into the darkness for his target, he froze at the sight of something that definitely didn't belong here.

A brief flicker of scope flare caught his eye a heartbeat before something struck him in the chest, causing a hollow thump to resonate through his body cavity. Slowly, he felt himself loosing power and before he knew it, he slammed into the earth, kicking up dirt and chunks of grass. Danny groaned, spat out some grass, and tried to pull himself up with one arm to look down at his torso. There he found a small circle-shaped device stuck firmly to his chest like a magnet, marring his DP emblem.

"It's a spectral energy neutralizer. While in contact with a ghost, it completely disables their ability to access their core. Not that I expect you to understand all of that."

Danny glared upwards, only to get the shock of his after-life. "Agent- Agent Alpha? I-is that you?" He'd only seen a glimpse of the man once several days ago, but he had heard what Agent O and K had called him.

Said man was standing above the downed ghost. He had on goggles that were similar in shape to his old sun-glasses and instead of a blindingly white suit, he wore a black one with small green accents along the lapels and pockets. Even his undershirt was black and had a green tie resting on top of it. "Why yes, it is."

"But I heard the Guys in White were disbanded after they nearly murdered those people at the observatory," Danny rasped out. He knew that he couldn't access his human half if his connection to his core was disrupted, so he took the time to look at the rest of his aggressors. He saw four men behind Alpha that were wearing similar attire, with ecto-guns in their holsters. They wore strange half-helmets with green visors and one of them was holding a larger weapon, most likely the one that Danny had seen before getting shot. His thoughts were interrupted quite rudely by a swift and powerful kick to his face. Danny grunted in pain as the hit caused him to roll flat on his back. A boot started pressing into his chest and Danny briefly wondered if the man could brake his ribs while he was in ghost form.

Alpha leaned down and a dim light reflected across his googles. "Do I look like I'm wearing white, ghost?"

Danny felt his mouth go dry at Alpha's response. Two of the four men behind Agent Alpha marched forward with metal rings that looked like restraints of some kind. "Wait!" He flinched in pain, feeling a throbbing ache go through his jaw. Dread settled inside him when he realized his healing wasn't working with the neutralizer on.

"I don't think so, ghost boy. We're finally going to rid the world of your kind." Alpha pulled away his foot, only to then pull out a trigger of some kind and press it.

Danny cried out in agony as the neutralizer on his chest activated and started to electrocute him. Both the weakness and electrocution was reminding him too much of the box that Vlad and Skulker had used on him in the past.

"By the way, you will only address me as Omega from now on, scum."

Danny felt his world slowly fade around him, slipping away from him like sand beneath him. His last thought was about how worried his friends and family would be and the last sight he saw was the dancing of fireflies in the woods. Then he blacked out completely.

Unknown Location. May 20, 2010. 14:05 CDT.

"He nearly looks human. It's pretty extraordinary when you think about it. An electrical complex of some sort that's controlled by a central energy node and forms something similar to a net to hold and mold ectoplasm into a specific form. Fascinating." Luthor stared up at the silent figure in the large tube they'd constructed around it.

"They're very deceptive creatures." Agent Alpha, or Omega, expressed simply.

"Yes. You say they can possess biological forms, machines, and theoretically other things as well?" Luthor asked, never taking his eyes off of the so called Phantom of Amity Park.

"Yes sir. We've constructed our own technology that simulates their powers of invisibility and intangibility, but-"

"It's not the same. Anything man-made would always leave behind molecular evidence or heat signatures, not to mention causing temporary blindness to the wearer if you managed to fully absorb all light. How does he do that, by the way? How can he see where he's going?" Luthor asked, seemingly to himself, and narrowed his eyes. Phantom had his eyes closed and was unresponsive behind the glass. His arms and legs were firmly secured to the top and bottom of the tube and a large metal muzzle covered his face from his nose down. Thin green lights pulsed through the circuitry of the restraints every few seconds.

Omega didn't seem to know Luthor was talking to himself and tried to answer. "We aren't sure how ghosts do it, but with more study, we can find out. We could start dissecting his body at this moment, in fact. My colleagues are prepared to-"

Luthor looked over sharply at Omega. "No. No invasive tests yet."

"Pardon?" Omega asked, impatience and irritation seeping into his voice.

"You heard me. I want to do some other tests. Could you imagine having copies of these things to keep order?" Luthor asked and turned away from Omega. "We wouldn't need to have people like the Justice League if we had the ability to manipulate these things."

"Hmph." Omega crossed his arms. "Agreed, but you do know that you can't copy a ghost, right? They have no DNA. And while there are mythological instances of ghosts being controlled by human masters, there's no modern science that could support such claims or make a device to do something remotely similar at this time."

"Then we'll just have to try to come up with something, hm? Until then, we'll send him to a safe place."

Omega frowned. "We're not going to experiment on him?"

"There's plenty of smaller and less powerful ghosts you can pick and prod at. We're freezing this one. If we don't freeze him now, there's no guarantee that our limited supply of ghost technology we've managed to scrape together will keep him in our hold. I'm going to be working on finding another more reliable supply of ghost technology. In the meantime, some of my other scientists will work with yours at another location to see if he can be copied without the use of DNA. Didn't you say they have an ecto-signature or something of the sort?"

"Well, yes, but it's more like a wavelength of vibration that their core resonates at. I'm not sure having a core vibrated at a specific speed would create a fully intact ghostly complex."

"I guess we'll just have to try, won't we?" Luthor replied as he started to walk away. Omega looked up at Phantom's form as the liquid within started to turn an icy blue. "Besides, he's not going to hurt anybody from now on. If you really want to destroy him later, I'll let you. Just have patience, my friend."

"As you wish, Luthor." Omega then marched after Luthor as ice started to coat the inside of the chamber and darken it. Scientists stood around watching as the process took place.

Madison, Wisconsin. May 20, 2010. 16:00 CDT.

Vlad Masters paced past his hologram of Maddie for the fortieth time that afternoon. He was completely dumbfounded. Several days ago, Samantha, Tucker, and Jasmine had barged into his Madison home, guns poised, and had demanded to be told where Daniel was. This had lead to a long argument in which Vlad tried to tell them that he hadn't been near the little badger for quite some time, since the attempted cloning, that was. He was still pretty peeved about that one.

At first they hadn't believed him, which was understandable. He had then shown them through his castle and told them repeatedly that if he had captured Daniel, he would be here since his Colorado home was still receiving repairs from both Daniel and the clone's rampage there. Eventually they had come to believe he indeed did not have Daniel. Vlad was surprised to ultimately find out that the boy had been missing for four days.

After they had left, Vlad had called on Skulker and threatened the ghost within an inch of his afterlife to tell him if he knew where Daniel was. Afterwards, he'd become fairly confident that the hunter hadn't captured or killed the boy. Now it was a only matter of time before the kids would eventually have to tell Jack and Maddie the truth and that would possibly lead to his own secret being revealed. At the same time, he was fairly certain that even if they found out, the kids would have enough sense to warn the two parents of his power and how he could crush them both, even his precious Maddie, if they dared rat him out. They also didn't have physical proof nor their little ghostly protector if they did feel particularly brave, or stupid. Either way, he would soon be done creating his Plasmius bugs and would be able to both, be up to date on Daniel's case and know if the elder Fentons knew about his or Daniel's other halves.

So then he was back to square one. All he knew for certain, and only because of the kids, was that Daniel had gone missing after going on patrol. Valerie would've told him if she'd destroyed the ghost boy, Skulker would've told him, any other ghost would be gloating about it, even the Fentons themselves would be gloating about it if they hadn't figured out they'd murdered their own son. That only left a few opinions. He could've gotten lost or hurt somehow, which was unlikely. Perhaps some other human psycho had stumbled upon him and managed to dispatch him, though that was also unlikely. The boy might've run away, but there were too many things about that that went against Daniel's character. Besides, he most certainly would've come to his mansion if he had needed someplace else to go; that much was obvious in Vlad's mind. The only people he could think of that would actually be quiet about capturing the ghost boy, would be the Guys in White, but they were recently disbanded by the government after their foolish attack on a teenager at the Amity Park Observatory.

It was as if Daniel had simply disappeared. There had to be something he was missing…

Ring~ Ring~

Vlad huffed and walked over to the nearby phone in his living room. "Masters residence." He was silent as he listened to the reply on the other end. "Ah, Lex, my friend. To what do I owe the pleasure?" He mentally arranged his pieces on the board once he knew who he was dealing with and waited to see what move the opponent would make.

As he listened, he grew more curious about what was being discussed. After all, he knew more about his friend and his business ventures than Luthor knew he did. This was curious, curious indeed; he settled in for a intriguing game.

Washington D.C. July 5, 2010. 1:44 EDT.

"What sub-level is this again and why are we here? I thought we agreed that it was okay for Guardian to tell us if he found anything fishy in the other sub-levels?" Flash asked. The speedster sighed and rubbed his head a bit as he walked out of the elevator behind Batman and Martian Manhunter. He really needed to get something to eat soon; it had been a long day and night.

"Sub-level sixteen. Do you remember when I said I was suspicious of Cadmus? The reason is because of a shipment they received recently. The short version is that some of the information about it didn't add up. I asked Guardian if he knew what floor it was delivered to," Batman replied gruffly. He honestly had a head-ache too. The battle against Wotan hadn't been easy, then they'd discovered that their protégés had run off and that Cadmus was worse than he'd anticipated.

"Care to do a quick sweep, Flash?" Manhunter questioned softly.

Flash nodded. "You got it." He stuttered into a false start before looking over his shoulder. "Are you going to tell me what I need to look for?"

"I'm not positive. I suggest we just search the floor thoroughly," Batman answered. Flash zipped off and Manhunter got the man's attention.

"I do sense something… odd."

"Like what?"

"It's a large bundle of… I'm not sure how to best describe it to someone who's not an empath or telepath, but it's like a large collection of emotion with no human consciousness attached."

"Lead the way," Batman replied curtly, watching as his ally floated in front of him and took point. It seemed like several minutes before they came to the first door in the long hallway. Once the door was opened, using a key card from Guardian, they spied a large frozen chamber in the center. Carefully the two heroes walked forward. They felt a gust of wind and Flash's voice cut through the silence.

"Another clone or something?"

Batman hummed. "It's definitely something." He walked over to the monitor and typed in a few things. After a minute of work, he glanced up at the pod and narrowed his eyes. "Well that explains things. I've wondered what happened to you."

"Huh?" Flash asked and walked closer.

Batman looked over his shoulder at the two other Leaguers. "For some reason, they have the Phantom of Amity Park down here. He went missing about two months ago."

"The ghost, from that creepy ghost city?" Flash questioned.

"I recall that we had been watching him since he appeared. That was right after those two scientists managed to make a portal into another realm, correct?" Manhunter continued.

"Yes. He's a solo-act. According to the media, he was the one that freed Amity from being trapped in the Ghost Zone last year. He also stopped a ghost from taking over a satellite-"

"You mean the one that caused all that crazy stuff to happen earth-side?" Flash questioned, now growing a bit more serious about the situation.

"The same." Batman eyed the chamber again before he walked over and wiped some of the ice from the outside, giving the heroes a slightly better view of the being within.

Manhunter observed the ice-dusted boy and a hint of remorse filled the martian's being. "He doesn't look much older than Aqualad or Kid Flash. I wonder how long he's been… a ghost."

"Hard to say. Ghosts aren't always souls of the deceased. That's according to the current experts," Batman offered in response.

"So what do we do? While we're fairly sure he's a good guy, we can't be sure that he won't go nuts if we release him. We also can't just leave him here," Flash expressed.

Batman gestured to the door, which was behind them, with his head. "Go hide in the hallway. I have something on me that can to protect me from his abilities. I'll release him and see if he's hostile."

Flash and Manhunter exchanged a glance before they nodded to Batman and exited the room. Batman glanced down and pressed a button on his utility belt, before he started to type in the commands that would release the cryogenic hold the tube had on the ghost. Once the ice had thawed, he saw the large clamps and muzzle on the ghost and furrowed his brow. He supposed the muzzle was to prevent Phantom from using his powerful wail ability. Finally he released the final lock and Phantom's arms fell from the clamps. The ghost then fell to his knees, slumped over and still unresponsive. After a moment, Batman creeped forward and worked with a lock-pick to unlock the muzzle from the ghost's face. The muzzle clattered to the ground right before a bright white light startled the Dark Knight.

When the light faded, Batman was fairly surprised to see a black-haired boy in place of the ghost he'd just freed. "So, I wasn't coming up with false theories after all. I was starting to wonder." He leaned down and tried to touch the boy, only to see a shock of green go across his smaller body and make him seize slightly. "So my belt still hurts you in this form…" Batman reached back and flicked the button on his belt off before lifting the unconscious boy into his arms. "This explains why you vanished with Phantom."

He came out of the room and Flash showed his surprise, while Manhunter seemed stoic as ever. "Whoa, what?"

"We'll talk about it later."

"So wait, the Phantom of Amity Park is a kid? Like an actual living kid?" Flash asked and looked at the boy that couldn't be much older than his Wally.

"I had had some suspicions but they were never well supported ones. It wasn't until Daniel Fenton was reported missing that I really considered that it wasn't just a theory. If his parents hadn't been the ones to actually create the Ghost Portal, then I might have never guessed he wasn't as he appeared."

"What shall we do?" Manhunter asked.

Batman frowned. "I suppose we'll have to ask him when he wakes up."


This should be the shortest chapter, seeing as it's kinda a prologue. The others should range between six to eight thousand words, roughly.

Hope you enjoyed it.