Summary: With the Justice League compromised, it is up to Young Justice to save the day.

Author's Note: Based on a 2-second preview of YJ Season 1 Finale that I saw with Batman fighting Robin. Although I had meant this to be a one-shot, due to several requests, I decided to expand the story. And yes, I've changed the first chapter slightly.

Disclaimer: All characters belong to DC, Time Warner, and CN; this is an original story that doesn't intend to infringe on their copyright. Feedback is welcome.

Copyright: December 2012

~ / ~ / ~ / ~

Alpha-Omega Protocol

By Syl Francis

~ / ~ / ~ / ~

Red Canyon Testing Range, TX-NM Border

Day 1/0900 EDT

~ / ~ / ~ / ~

The Justice League attacked without warning. The Young Justice junior heroes were taken by surprise by the very people who knew both their strengths and their weaknesses—their mentors. The team had been deployed to the Red Canyon Testing Range, a remote missile proving ground located along the Texas-New Mexico border.

Just that morning, the Team had assembled in Mount Justice for a mission briefing. Batman showed them security camera video of a previously unknown terrorist group in the act of attempting to steal two strategic nuclear missiles…

"The mission," Batman had told them, "is to stop the group at all costs. Under no circumstances are those missiles to fall into the hands of an unknown enemy."

"Uhmm…Batman, sir?" Kid Flash dared speak up. Batman merely gave him his infamous glare. "Uhmm…what, if anything, will the League be doing, while we're…uhmm…so totally risking our lives? Sir?"

Batman grinned in amusement at the question, which in hindsight should have been the first clue that all was not right with the situation. "The League is currently monitoring the situation and staying apprised of the activities along the Texas-New Mexico border. You kids have nothing to worry about." The fact that Batman took the time to answer a Wally question should have been their second clue. Their final clue, as Robin would point out later, was that Batman called the kids. Something he would never do. As it turned out, the mission was a just a ruse to get the team out in the open…

Robin flipped backward faster than he'd ever moved, just barely evading the Dark Knight's kick. The Boy Wonder had already managed to dodge a couple of batarangs. To his shock, he realized that the force behind the strike had not been meant to incapacitate, but rather to kill.

Around him, the rest of his teammates also had their hands full, each engaged in a deadly dance with their own mentors.

Kid Flash swerved in time to avoid tripping over the Flash's right foot; at the speeds they were going, an accident could have resulted in a broken leg. Miss Martian dematerialized just as her uncle, Martian Manhunter, flung a huge boulder at her—another narrow miss.

The others weren't faring much better. Artemis had not one, but two archers—Green and Red Arrow—to defend against. Aqualad was barely holding off Aquaman with his water bearers, and Zatanna found herself facing not her father, but Dr. Fate—a Lord of Order against whom she stood little chance.

And the new kid, Rocket, flew in a zigzag pattern at supersonic speeds, weaving a complicated tapestry of contrails that showed her desperation as she somehow avoided her mentor, Icon. This wasn't how they had planned to celebrate his recent induction into the League.

Aqualad, realizing that the team was in serious trouble, sent out a retreat order through their psychic link. "Everybody…break off and regroup in the bioship!"

"Roger-dodger!" Kid Flash.

"'Bout damn time!" Artemis.

"On my way!" Miss Martian and Zatanna.

"Save me a seat!" Rocket.

"Gotcha!" Robin. Then, "Uh-oh!"

As the others managed to breakoff and make their way to the bioship, they heard Robin's unmistakable "Uh-oh!"

"Robin!" Aqualad called over the link.

"A little busy…!" Translation: Don't distract me—I'm fighting Batman!

"M'Gann…Go!" At Aqualad's order, Miss Martian flew the bioship over to Robin's last known location.

~ / ~ / ~ / ~

Red Canyon Testing Range, TX-NM Border

Day 1/0930 EDT

~ / ~ / ~ / ~

Robin leaped backward, as far away from Batman as he could get. He used a nearby boulder as a springboard, just barely avoiding yet another deathblow. Unfortunately, Batman suddenly snatched Robin's cape and pulled hard. The boy's forward momentum was abruptly halted, and Robin felt himself being unceremoniously hauled back.

The next thing Robin knew, he was slammed on his backside onto the rock-strewn ground. He hit so hard that the air in his lungs was forcibly expelled with a loud ~whoosh~!

"Okaaay…that hurt," Robin muttered.

Batman held the junior hero down with one hand splayed on his chest, applying painful pressure, making it difficult for the boy to breathe. If he pressed any harder, Robin's chest was in danger of caving.

But as precarious a position as that was, it was the least of the Boy Wonder's worries, for Batman's other hand was holding a razor sharp batarang against the teen's throat.

Robin squirmed frantically, beating his hands ineffectually on Batman's arms. He suddenly felt very small and helpless, a feeling he hadn't experienced since the terrible night his entire family had fallen to their deaths in front of him. He hadn't been able to help them either.

A grim determination came over him. He wasn't that same helpless kid anymore! He was Robin the Boy Wonder—the Dark Knight's partner!

He had to break Batman's hold, but his more experienced opponent only increased the pressure. Stealthily, Robin moved his right hand to his belt, reaching for one of his pouches. If he could just press the release catch—

The next instant, he felt a sharp pain in his neck, indicating that the batarang had broken skin. He felt a wet trickle start down his neck. Grimacing, he looked up Batman, frightened of his mentor for the first time in his life.

Batman gazed back, his expression grim, displaying no remorse at what he was about to do—just cold satisfaction.

"You forgot who trained you." He spoke in a low, raspy growl. "Did you really think you could beat me?"

"Batman…please! Don't do this!"

Batman applied more pressure, but he was taking too long. Robin realized that if Batman really intended to kill him that he would have been dead already. Maybe…?

"Bruce…?" Dick reached a free hand up to his mask and yanked it off. His dark blue eyes gazed pleadingly into his mentor's eyes—no, into his father's eyes. "Please, don't do this. It's me…"

Before Robin could react, Batman released the pressure on his chest and grabbed his arm, twisting it painfully, almost pulling it out of its socket. Dick gasped at the sudden pain and spoke through gritted teeth.

"You promised…" (You'd take care of me, he left unfinished.)

Batman froze, staring intently at his prisoner. Gone was the cruel, cold stare. The Dark Knight's mouth was drawn into a grim line, his jaw clenched. Dick could see the intense inner struggle that Batman was undergoing. The hand holding his arm tightened reflexively, but the pressure on his neck slowly eased.

Batman blinked.

"Dick…?" He spoke as if he'd just awakened from a long sleep. "What—?" He gasped in sudden pain, holding his hands up to his head. "!"

"Bruce, what's happening?" Dick had stumbled to his feet, his usual graceful moves affected by the pain radiating from his shoulder. Awkwardly, he assumed a defensive stance. He looked uncertainly at his mentor who only moments ago had been set to slit his throat.

"Get away! Now!" Batman scrambled away from his protégé on his hands and knees, putting distance between them. "The League's compromised…Vandal Savage…bio/nano tech!" Each word was a struggle to get out. "Alpha-Omega Protocol…Go!"

Robin's eyes widened and he took off at a run. Alpha-Omega Protocol meant the Justice League was compromised by unknown forces—the members were being held under some kind of mind control. They couldn't be trusted. It was up to him and his teammates to bring them down.

They were on their own.

A loud, angry roar behind him told him that Batman had lost his internal battle to wrest control from whoever had taken him over. He heard the sound of heavy boots pounding and ragged breaths gaining on him. He dared a quick look back over his shoulder and knew he'd run out of time. His nimble fingers pulled three smoke pellets out of his utility belt.

Unexpectedly, he spun suddenly on his heel and tossed the pellets. On impact, they released a harmless, opaque smoke that concealed his movements. He then executed a series of complicated tumbling moves, and with the momentum gained, leaped onto Batman's shoulders. Using them as a springboard, he quickly somersaulted off. In the blink of an eye, Robin pressed a hidden switch on his right gauntlet, which fired his specially modified Taser.

As the two wire leads latched onto the Dark Knight's chest, a non-lethal current flashed toward Batman to no effect. His uniform was insulated against the very Taser that the Boy Wonder had used against him. Batman gave him a knowing smirk and was about to pull off the wires, when Robin pressed the hidden switch in his glove a second time. Instantly, a secondary current with a much higher voltage was sent out, negating the Batsuit's countermeasures against the Taser's original settings.

As per the Alpha-Omega Protocol that Batman had conceived in case any member of the Justice League should ever go rogue, taking down his own mentor was something that Robin had devised and trained for extensively. The second, stronger current was a counter-countermeasure that he and Alfred had built into the Boy Wonder's gauntlets without Batman's knowledge.

Batman abruptly halted in his steps, his body jerking as the voltage affected his nervous system. Robin stood for just a moment longer and watched as his mentor collapsed in place.

Running toward the fallen hero, Robin took out a syringe and quickly plunged it into a vein. He withdrew a blood sample and slipped it into a specially insulated belt pouch. Fighting the urge to stay and render Batman aid, he took off toward the last location of the bioship.

The others were probably already on board. Almost as soon as the thought came, an opening appeared out of thin air about 20 feet in front of him. Kid Flash stood in the open hatch of the cloaked bioship, urging him to hurry.

"Come on, Robbie! We gotta get outta here!"

As Robin boarded, he took one last look at his unconscious mentor and made a silent vow that he would free him and the rest of the Justice League of whatever mind control had taken them over.

He knew what he and his teammates must do:

Step 1: Find a safe house.

Step 2: Analyze the blood sample for any signs of a chemical or biological agent or nanotechnology.

Step 3: Develop countermeasures and/or an antidote.

Step 4: Take down Vandal Savage and his allies.

Step 5: Order pizza and celebrate their victory.

Okay, Robin admitted, maybe I'm getting just a little ahead of myself.

There was no way the junior heroes could take on the whole League and win. There just weren't enough of them and the League was too powerful as a group. Unfortunately, the Alpha-Omega Protocol was only a last resort scenario. The methods that Batman had planned for taking down the individual heroes were designed to debilitate and possibly kill.

Robin didn't think they were there yet. He would initiate the Protocol as a last resort—just as it was designed. No, they had to concentrate on finding out how Vandal Savage had managed to take control of the League and initiate an effective defense against it.

Otherwise they were faced with the very real problem of having to take down each JL member individually. Of course, when he thought about it, the team wasn't all that stood between the JL and possible world domination. There were other heroes out there. The next moment, he discarded the idea. If the Justice League, the World's Greatest Heroes, had been compromised, there was a very good chance that the rest of the world's heroes were too.

These thoughts ran through Robin's mind as he strapped himself to his seat. It was time to go to work.

"What are we going to do?" Artemis was saying. "Did you see them? If Aqualad hadn't called a retreat—"

"—If he hadn't called it, we'd all been toast!" Kid Flash said angrily. "I can't believe that Uncle Barry—"

"They are not themselves," Miss Martian said quietly. "I tried to reach Uncle J'onn telepathically, but it was as if his mind was blocked. There was something preventing me from reaching him."

"The League has been taken over with some kind of mind control," Robin said quietly. "Batman broke through for a brief second—enough time to warn me." He glared at the others. "We need to go somewhere safe and regroup. It's too dangerous to return to Mount Justice. And at this point, the Batcave, Atlantis…all of our usual safe houses are also out of the question."

"But where?" Zatanna asked. She was obviously upset that she had barely escaped Dr. Fate's mage bolts, refusing to accept that the powerful sorcerer was her father.

"I know a place," Robin said quietly. "But first…there's someone I've gotta call." He quickly tapped his fingers on his virtual computer and a scrambled image appeared.

"Master Robin? What is it, young sir?"

"This an Alpha-Omega priority. Make your way to the alternate Batcave ASAP."

"I take it Batman and the rest of the Justice League—?" He left the rest unfinished.

"Roger. And Alfred…? I'm bringing friends."

There was a brief pause on the other end. The scrambled image immediately cleared and Alfred's kind, concerned face replaced it.

"I understand, young sir. I am evacuating even as we speak. I shall meet you at the rendezvous."

"Right…see you there."

"And Master Robin…? We shall get through this." He gave Robin an understanding look and cut the transmission.

"Uh…Robbie?" Kid Flash said uncertainly. "Aren't you kind of…y'know, exposing your whole secret ID thing?"

At the others' nods, Robin sighed while taking in their curious expressions.

"Batman always said that in the case of a global emergency, if the League were compromised or couldn't help, then..." He shrugged. "I guess this qualifies." He removed his mask and gazed at them with his dark, piercing blue eyes. "Hi, my name's Richard Grayson, but my friends and family call me Dick."

Artemis let out a small shriek. "I thought I recognized the old guy! He picks you up like everyday after school. Wait! You? You're Dick Grayson, the geeky mathlete that's like the smartest kid in the whole school? Bruce Wayne's kid? The same little freshman who took a picture of us my first day at Gotham Academy? That Dick Grayson?"

Robin nodded. "Yeah…told you we'd laugh about it one day." He paused and looked suddenly ominous. "Guess today isn't the day, huh?" He turned to Miss Martian and sent her a set of coordinates. "M'Gann, prepare to receive coordinates to our destination."

End of Part 1

~ / ~ / ~ / ~