AN: This is my take on a third season to a show that should have been renewed. I will do my best to keep with what the show has done but will add some changes to character origins and powers, kinda like what they did in the show with Garfield, Conner, and a few others but it (hopefully) won't be too out there for the fans of the series. This will also work as a sort of sequel to my earlier story collection 'Breather' and will take some happenings from there since each chapter occurred between the episodes, so any newbies may want to take a look at that one so parts of this can make sense. So, without further ado, please enjoy.

Young Justice: Darkness Falls

By: Angelus-V1

Part 1: New Addition



July 5, 05:16 UTC

For the past few hours, the space station known as the Watchtower, once secret base to the Justice League and now known to the residents of Earth, has been quiet with most of the world's protectors having left for home or being deployed on a mission. The only exception to this were two of the members from the League's black ops force known as 'The Team' who were on monitor duty, providing the only break to the silence with the occasional small talk or issuing of orders.

Currently, Batgirl was at the helm of three large computer monitors with a large curved holographic table in front of her. Two keyboards were situated before her to relay messages to Beta and Gamma teams as they carried out their assigned missions with a display of an overhead view of the cities they were in showing their positions on two of the screens. The third screen, which took the top position was reserved for Alpha team and had a video feed of the interior of M'gann's bio ship.

"Alright, all squads are looking good," Batgirl said as her fingers nimbly moved over the keyboards. Years of being a partner to both Batman and Nightwing have taught her how to work several computers at once, an advantage if she were required to hack into several databases simultaneously.

"Tigress, what does your team's time look like?" Aqualad asked over their secure channel.

"Okay for the moment," came Tigress' voice from the left side monitor. "Lex had a few extra traps that were not expected but we managed to get around them. Bumblebee's already hacking into the computer server from his main office and Kid Flash is skimming through his paper files."

"Estimated time until you're done?"

"Um, give us about another three, four minutes to download everything. Bee's having a time getting past the firewalls."

"Roger that. If you need any assistance let us know. Keep in contact."

Moving to the second monitor, Batgirl brought up a schematic of one of Lex Corp Farm's main factories in Smallville. There, Gamma team was investigating the rebuilding of the plant and what further secrets Lex was keeping that were not in the plans. Their mission was to find clues on what Vandal Savage was now planning as well as his whereabouts, which led them to their current position.

"Batgirl to Gamma, come in."

"Gamma here," Robin answered. I've just moved in with Static to investigate the ground floor of the facility and have picked up residual Boom Tube energy. I sent Lagoon Boy to the nearest lake to get samples of the water in case there's any dumping going on. Wonder Girl's our backup and is taking position in the nearby cornfield."

Coming up behind Batgirl, Aqualad placed a hand on her shoulder. "Tell Lagoon Boy to be careful when he goes in the water and to not jump the gun. He still has a lot to learn on patience and trust as well as what it means to work on a team."

As Batgirl relayed their leader's message, Aqualad looked upon the only screen with nothing but an empty room on it. Pulling up a holographic keyboard of his own, he brought up the bio ship's com system and called for the three members making up Alpha Squad. When they didn't answer, he tried raising them again until M'gann came on screen with Garfield close behind her.

"Um, we're here, Kal…Aqualad," the Martian said as she wiped her eyes. "We just needed a minute."

"Is everything alright? You are about out of the Watchtower's communication field and I need to make sure everything is going smoothly." By this time, Conner came on screen and sat down with a bottled water in hand.

"Everything's fine, Aqualad. Like I said, we just all needed a moment.

Seeing the puffiness around her eyes and how Garfield was wiping at his, he knew what their momentary disappearance was about. Even though Conner wasn't one to show his feelings like the others, Kaldur knew from his body language he too was still mourning the fallen Wally West. "Understood. The moment you get beyond the moon, communication will cease. So stay in touch until then."

"Copy that. Alpha team, out."

With everything going smoothly for the time being, Batgirl stepped back from her position and looked at the team leader. "So be honest, how does it feel to be back in the saddle again?"

"To be perfectly honest," Aqualad answered as he crossed his arms, "I was not expecting this position to have been given back to me so quickly. I was sure Nightwing would stay in command for a time, or at the very least, take charge of half the team."

"You do know why he put you back in command right? He said he isn't exactly cut out to be team leader after all he's been through and the decisions he's had to make."

"Do you have any idea where it is he was headed off to?"

"None whatsoever, he doesn't really talk to me all that much."

"If you do not mind my asking, why are you two so distant despite being under the tutelage of Batman and partners?"

"Story for another day, boss man. Story for another day."

Lex Corp

July 5, 05:21 UTC

"Okay, download almost complete. Just another minute or two," announced Bumblebee as she sat back in Lex's extravagant leather chair.

"Good, because I'm having a really bad feeling about this." Tigress, with the aid of a small rectangular computer screen, kept her eye out for anyone looking to interrupt the trio. Before anything was started on their end, she had planted two button sized cameras in the hallway to monitor the presence of any late night workers. "I haven't seen anyone, not even a janitor and it's giving me the feeling like we were expected to be here."

"Well if we were, I would so totally be enjoying the view," the new Kid Flash said as he stood before the large windowed wall overlooking Metropolis. "Hey, how much do you think he spends on carpeting in this office alone?"

"Not really a good time for financial discussions," Bumblebee said. "Jump drive is just about done…and…fini…wait, I didn't see this file before."

Bringing up a file marked 'PKR16' the insect themed heroine quickly browsed through the folder's files until settling on a familiar word.

"Hey, Tigress, isn't Superboy a type of genomorph?"

Without taking her eyes off the screen she was using, the blonde answered, "Uh, I think I heard Wally say that about him at one point. Why?"

"Well because, this file has stages for a genomorph codenamed Project Kr"

"That's Conner alright." Leaving her position beside the door, Tigress went to look at what Bumblebee had found but also kept an eye on the small screen she carried. "What does it say about him?"

"Well, it has files on three stages of his development. The first stage looks to be when he was cloned and force-grown. The second looks to be the unlocking of some of his Kryptonian powers. Strength, invulnerability, micro and infrared vision, and hearing. It was all they could unlock naturally."

"Does it have anything about something called Shields?"

"Let me check." Letting her fingers fly over the keyboard, Bumblebee searched high and low for what her partner asked. "No. Not here at least. But it does have what the third stage was before his, 'liberation', as it puts it."

"So, what was the big guy gonna get this time?" Kid Flash asked as he zipped over to the two.

"I can't tell. There's so much to cycle through," Bumblebee told him. "I have to save all this and go through it with Batgirl later."

Just then, Tigress' earpiece came to life with Guardian's voice. "Guardian to Tigress, come in Tigress. Over."

"Tigress here. What's the situation?"

"You need to get out now. It looks like Lex's limo just pulled into the building. He didn't stay out for long."

"Roger that. Bee, how much more time do you need?"

"I need about another forty five seconds," Bumblebee informed her.

"Kid Flash, head on up to the roof and make sure our way out is still secured. I'll stay with Bumblebee till she's done."

"Gotcha'." Faster than either girl could blink, Kid Flash shot out of the office and into the air ducts to get back to the roof.

"And that does it. Now to just shut the computer down aaaaaannnnnndddddd…there. Let's go." Shrinking down to her much smaller size, Bumblebee flew into the air duct with Tigress close behind.

Once back on the roof, Guardian signaled for the three to make their way back to the rendezvous point. Kid Flash ran down the building, across the street, and up the opposite building, arriving beside Guardian faster than Bumblebee could. Tigress got out her pully device and slung it around the cable she used to get to the roof of Lex Corp. A small rocket on top of the device fired and propelled her forward at a high rate of speed. Once on the other side, she pressed a switch on the cable's mount and waited for it to retract back to her.

"Okay, mission accomplished," Tigress told the others as Sphere came flying over to them in her super cycle mode. "Let's get back to the Zeta Tube and to the Watchtower."

As the group of infiltrators took off on the sentient cycle, none knew they were being watched closely by the owner of the building, Lex Luther himself. Sitting back in his leather chair, he monitored the entire episode from his private panic room via a large HD monitor mounted to the wall. Pulling out a keyboard from a large redwood desk in front of him, he pulled up everything the young heroes downloaded and copied.

"Children," he said with a sly smile, "when will you all learn, I control what you see and do?" He then relocated the files he wished for them to find back to their original places and shut his computer down.


July 5, 06:59 UTC

It was a very peaceful night in the farm town of Smallville. Crickets made their high-pitched buzzing songs, the wind swept through the tall stalks of corn, and the stars were shining brightly overhead. All in all, Wonder Girl was board.

The protégé of Wonder Woman knew this was going to happen when she was told to stay hidden and provide backup if needed, but didn't anticipate it taking this long. According to Robin's wrist mounted computer, to which they all synched their watches to, dawn was only twenty three minutes away. It was a fact that made her anxious to get out of there or move in and bust some heads, but she knew she had to stay in her position should she be called. She was actually so intent on making sure she was the perfect choice for back up, she neglected to see a gray and black snake slither towards her.

Keeping her eyes and ears out for any sign of trouble, she stayed in a kneeling position with one hand on the ground. Hearing a rustle to her left, she turned to attempt to get a better view through the stalks when she felt the scaly body of the snake slide across her fingers. The sudden realization of the reptile made her eyes grow wide and forced her to jump back while making something akin to a yelp.

As she fell backwards, a few stalks of corn separated and out stepped Lagoon Boy who was also startled by the Amazon's fright. He fell backwards as the fins on his face popped out more and in turn, made Wonder Girl yelp in fright at his face. He then let out another yelp when they both realized there was nothing to be afraid of.

"Neptune's beard, you scared me," Lagoon Boy said as he gripped his chest. "What were you doing?"

"Waiting for the others when a snake crawled on my hand." Standing and shaking from the feel of the reptile Wonder Girl added, "Ugh, I hate slimy things."

"Gee, thanks."

"I just do."

"Hey," came Robin's voice. "What's going on over here? This is a stealth mission, keyword, stealth."

Meeting up with the other two, Robin and Static looked both of their frazzled teammates over.

"She got scared by a snake," Lagoon Boy explained.

"Snake, where's the snake?" Static asked as he moved rather quickly away from his spot.

"Oh for Pete's sake." Bending down, Robin picked up the terror of the cornfield and gave it a look over. "It's a harmless Prairie Kingsnake. It's not even poisonous."

"I don't care," Wonder Girl said.

"Just get rid of it," Static added.

Setting it down with a chuckle, Robin looked his team over. "You're superheroes with actual super powers. And Wonder Girl, if it bit you it would have broken its teeth."

"I don't care," she repeated. "I just don't like slimy or scaly things."

Shaking his head, Robin let out a sigh. "You're lucky I like you. Now let's get back to the Kent farm and to the Zeta Tube the League just had put in their barn. We found two underground floors only accessible with Boom Tube and traces of someone using them to get in and out. Maybe Savage, maybe not, but it's a lead. We just need to report back to the Tower and see where this fits in with his hijacking War World and taking it to Rimbor."

Taking off before the sun could rise, the group made their way through the corn field as quick as they could to meet back up with Blue Beetle at the barn.

"Seriously, I can't believe you two are afraid of a little snake," Lagoon Boy said as they began to make their way through the cornfield. "Couple of cowards."

"Hey, fishboy," Static said as he ran beside him. "Don't make me call out He Who Walks Behind the Rows."

The three noticed Lagoon Boy looking around more and running a tad bit faster after that.

Bio Ship

July 5, 09:30 UTC

For the last ten minutes, Conner had moved to the cargo area of the ship. Nine hours being cramped up in the Martian space machine was making him restless. Unlike the past trips he took with M'gann to her home planet, this one seemed to go much slower despite traveling at the same speed as always. The first two hours went by too fast for his taste as Garfield got a lesson on piloting the vessel and took the opportunity to have it perform barrel rolls, loops, and spins. It was exciting having the young boy live out his sci-fi fantasies until they got past the moon and M'gann had to put the ship on autopilot for safety reasons.

After using one of the shelves in the back to help stretch his arms out, he rotated his neck and headed back to his seat. By now he had worked out the cramp trying to settle into his left leg as his heavy footsteps echoed throughout the ship.

"Conner," M'gann whispered, drawing his attention to where she stood at the front of the ship. "Can you be a little quieter, please? Gar's asleep."

Looking at the chair the boy occupied, he saw him slumping in his seat with his arms hanging loosely and legs stretched out as he snoozed.

"S…sorry." Taking more careful steps, the hybrid made his way over to his seat and once again sat down when he felt an all too familiar nudge at his mind.

It had taken him some time to bring himself to trust her enough to let her back in after she tried to make him forget why he was angry at her so many months ago, but slowly, he found himself just wanting to feel her presence in his mind more and more. It was a feeling they had come to appreciate at the beginning when it was just the two of them in their old home, Mount Justice. Since then, it became something more as they pursued a relationship, the happy Martian and the Brooding clone. It was a way to be intimate with each other when they couldn't be physical in the moment.

"Yes?" Conner answered mentally. Before, he had let her in freely, now she made sure it was okay to enter his mind and despite what she had done, he more than wanted to open up that part of himself completely to her again, just not yet.

"Would you like for me to dim the lights?" M'gann asked. "It would be easier to fall asleep until we get there."

"If you don't mind."

With a mental command from the Martian pilot, the overhead lights dimmed until it was just visible in the ship. The lack of light had another effect on them as they instantly remembered what they would do on the long trip to and from Mars when they were still in a romantic relationship but now, they were back to square one.

"Mind if I ask you something?" M"gann asked.

"Go ahead." He uncapped his drink and took a sip.

"Back at Watchtower, when you mentioned having the courage to…you know."

"I just thought they had the right frame of mind. What Artemis and Wally had…it's hard to come by."

"Same could be said about what we had."

Looking up at her, he nodded. "You told me on Rimbor it was your fault what happened between us. It wasn't all your fault. I should have stayed and worked it out with you instead of running. It was just…with everything Cadmus and Luther's done to me…it was just easier to leave than work it out."

"Conner," she walked over beside him, "if you really believe that, then please believe when I tell you the reason why I tried to make you forget was because I never wanted to lose you. We were still learning about being in a relationship and I didn't know how to, well…I just let my powers get the best of me. I should have stopped and listened to you, stopped for you. And instead, I messed everything up."

"But what about-"

"Rebound guy. We never got close to what you and I did. I'm…actually surprised you and Wendy never…I was certain you two were-"

"Well, Wendy really isn't my type." He reached out and took hold of her hand. "I like my girls green…or white."

The two shared a smile in the moment as the bio ship continued on its course, not knowing a certain monkey boy had his eye partially open with a grin on his face.