So, Chapter 1. I actually finished it.

First, I'd like to thank Fun Time Special, Illyria Lives, and Eppo-pink-skuller-fly-fangirl-XDXDX for reviewing. I realized that with the PoM fics being updated as fast as they are, my story gets pushed to page two by the next day, so not a lot of people probably even noticed that there's a new story out. Well, I guess I'm lucky to have three kind reviewers. Thanks again, guys!

This chapter could be a little boring, mainly because I'm using Chapter 1 to explain my world and introduce some of the cast. The episode-rewriting will start next chapter. I promise.

Disclaimer: The Penguins of Madagascar does not belong to me, end of story.

Chapter 1

The Secret Operations Headquarters was not a place you would find listed on the local phonebook. That is, given that you've even heard about this place in the first place. Only a handful outside the Secret Ops even knew this place existed. And about half of that was dead.

By complete natural causes, of course.

But they had a good reason to be so secretive about their actions. They were on every criminal mastermind's "eliminate when sighted" list. But despite their good intentions, they were also on NYPD commissioner's "capture if at all possible" list. Now how is it possible that a group of people are hiding from both sides of the law?

Simple. Because the Secret Operations is a group of vigilantes.

Team Penguin was the action team of the Secret Ops. If there's a place to be broken into or people to be stopped, they were the ones you go running to. The four man team had worked together for six years and counting. Right now, they were on their way home, congratulating themselves on yet another successful mission.

Skipper was the leader of Team Penguin. At the age of 28, he was the best martial arts user among all the operatives. He's a natural born leader, with piercing sapphire eyes that dared anyone to disobey him. So far, only three people had braved the eyes.

Kowalski was Skipper's most trusted colleague. As long as he was not in the lab, that is. Though he was a year younger than Skipper, he had the intelligence that most grown man could only dream about. But despite all his knowledge, he was still prone to blowing things up by accident in his lab. Kowalski had a reputation for being the one to cause the second most explosions, losing only to Rico.

Now, Rico was a special one. He had lived in Secret Ops pretty much all his life. Perhaps it was due to his exposure to weapons and sharp objects at a young age, but over the years, he had taken a liking to explosives and swords. Now, when he held anything blade-like and explosive-looking, people knew they need to run. Fast. He also had the unusual ability to hide any weapon on him as long as he's wearing clothes. He's a walking weapon vault.

The last member of this team was Private. Of course, that's not really his name, but no one knew his real name. Not even Private himself. He's the youngest Penguin, being only 17 years old. Despite being well into his teenage years, he still had a heart of gold and innocence that no one could question. Not even Skipper.

They gave each other a series of complicated high-fives while walking through the door of an apartment building. The manager at the counter looked up, rolled her eyes, and placed her attention back on her computer. Private noticed her and waved, "Hey, Alice."

Alice waved at him without looking up. Private smiled. Alice may not be the nicest red-head around, but she was nice enough to him. Most of the time.

"Let's go, Private!" Skipper called from where the others were already waiting inside the elevator. Private quickened his pace and smiled apologetically, "Sorry."

The elevator door slid close as soon as the boy stepped in.

To any other person, this elevator couldn't have been more normal looking. And to any other person, the Emergency Button in the elevator was a circle you wouldn't want to touch unless you were in trouble.

But Skipper was not just any other person.

He didn't hesitate as he pressed the red bell image on the circle. There was a slight pause before the speaker came to life.

"You have pressed the Emergency Button. Please state your emergency." A robotic female voice sounded.

"Scan." Skipper said simply. Immediately, the button shone as it scanned Skipper's finger. At the same time, the voice identifier recognized his voice, and a bar of blue light projected from the lamp above them, scanning the enclosed space. It ran over the elevator's four occupants, reading their body build and jaw lines. After it was done, a tubular gadget came out from the wall beside them and took careful aim at their eyes. It was really a retinal scanner, and after it collected the data it needed, it disappeared back into the wall.

All that took less than five seconds.

"Operatives confirmed." The female voice sounded again, but this time it lost the robotic edge. "Codename: Skipper. Codename: Rico. Codename: Private. Codename: Kowalski. Please state your destination."

"Ground floor." Skipper announced.

"Destination confirmed." And with that, the elevator took them down.

Skipper gave a long whistle. "I'm still impressed. Love what you did to this cube, Kowalski."

Kowalski smiled. "Just did what I do best, Skipper." The elevator continued to descend as Skipper smirked and punched Kowalski lightly on the shoulder.

Of course, no one outside Secret Ops knew about the additional sub-level floors. To anyone who happened to be standing outside the elevator right now, the elevator had just stopped at the Power Room in the basement. But in reality, the elevator was already a good fifty feet underground.

The elevator gave a nice ding as it reached its floor. The four operatives braced themselves as the doors slid open.

"Hey, the Penguins are back!" Someone shouted from amid the swarm of people that were passing through the lobby. Immediately, they became the center of attention for about three seconds. People waved at them. Some smiled and winked. Others asked how their mission was without really wanting to know the answer. As soon as the three seconds passed, everyone was back to their own business again.

"Ah, the HQ." Skipper sighed with content. "It's good to be home."

"Well, if it isn't the Penguins." Another voice called out. The Penguins looked up to see a man with trimmed dark brown hair walking towards them. "Back from another successful mission, I presume?"

"You presume correctly." Skipper said proudly. The other man chuckled, "Well, I expected nothing less from our finest field team."

"Gee, thanks, Mason." Private said replied, a little embarrassed even though he really shouldn't be. "We're not that good. By the way, where's Phil?"

The one called Mason rolled his eyes. "He ran into some trouble trying to trick the Gorilla Twins. He's still at the med bay."

"Oh no," Private gasped. The Gorilla Twins were famous for their extensive use of brute force. There was only one person so far that ticked them off and got away with it. "Is he alright?"

"Please, if he went down every time someone pounded him, he wouldn't even be alive right now." Mason replied with a laugh. "Well then. I still need to file away this other mission. I'd better get going." They said their good byes and watched the man go. "Speaking of missions," Skipper said. "Let's report this one to Tom."

Tom was the chief of the whole Secret Operations. His great-grandfather had founded this organization, and as the years passed, the torch was passed down to him. He's been running Secret Ops for twenty years now, and he had to say that right now this place had officially reached its golden years. Everything was going smoothly, though they still haven't had any progress in getting the PD commissioner's trust. But that could wait.

Tom frowned at the piece of info that was just sent in from one of the undercover teams. If what was written on the paper was real, this could mean trouble. Or, it could just mean that a bored kid got too familiar with the Internet. Still, if this particular operative thought that this was important enough to send back, Tom knew better than to just wave it off as a false alarm.

There was a knock at his office door. Tom casually slid the paper into a folder and put it in the drawer as he called. "Come in."

The door opened, and Team Penguin walked into the office. "We've put a stop to that drug deal and triggered the alarm so the NYPD could find them." Skipper reported as soon as the door closed.

"I knew I could count on you guys." Tom said with a smile. "Great job, Penguins."

"But that's not all." Skipper stated seriously. "Rico!"

Tom raised an eyebrow when the scarred operative pulled out a gun-like device from seeming out of nowhere and placed it on his desk. Even after years of seeing Rico do that, Tom still hadn't gotten used to it. He could make a living as a magician. He thought. Gingerly, he examined the device.

"One of the punks tried to nick us with that before we took him out." Skipper explained. "Well, I'm not really good with these kinds of things. Kowalski, report."

Kowalski stepped forward and reached out a hand to ask for the device. As soon as Tom handed it to him, he began to expertly dismantle it. "It seemed to emit a highly condensed electric charge. Well, seeing the dial on this device, I would assume that there are different settings on it." He frowned when he read the setting. "And according to this, that kid had wanted to turn us to dust." He muttered almost amusingly.

"The device, Kowalski?" Tom and Skipper reminded him at the same time, one a friendly reminder, the other bordering on annoyance. Kowalski blinked and mentally shook himself. "Right." He returned to dismantling it, reporting his findings as he went. "The outer shell is made of a metal that's harder than titanium. Someone must have been making new alloys out there, because I've never seen this kind of metal. The device itself is built simple enough. It's actually easier to put together than an actual gun. No offense, Rico. Now, this must be the unit that contains its power source, if I can just get it opened…aha! Got it! Now let's see what…good Galileo!"

Private, having let his mind wander some time during Kowalski's report, snapped his attention back at the outburst. Skipper was immediately beside the tall scientist. "What is it, Kowalski?"

"I…I don't really know." Kowalski admitted. He pulled out a small cylinder that glowed with a green ring of light running through it at about one ring per second, staring at it in awe. "I've never seen anything like it. And coming from me, that's really something." He held the cylinder up against the light. "I'll have to run some tests in my lab."

"Then, go right ahead and do it." Tom stated. "Make sure you find out what it is." The scientist nodded. He carefully slipped it into a plastic bag he had with him and put it in his pocket.

"I think we all agree that this device is way too advanced for The Aces." Skipper said grimly. "Someone's been supplying them. And I think I know who it is."

Everyone immediately caught on. Private shifted nervously at the thought of that person. Rico and Kowalski both stared off into space, lost in past memories. Tom sighed. "Let's not jump to conclusions here, Skipper. It could be any other person that made this thing."

Skipper placed his hands on Tom's desk and leaned forward. "But Tom, if it really is him, we need to take precaution. A lot of precaution. You know just as well as I do about what he's capable of!"

"I know." Tom drew in a deep breath and let it out in a long sigh. "I know. We've lost too many men to him for me not to."

The room fell into silence. Everyone was thinking about what was just said. Finally, Tom ran a hand through his graying hair and sighed yet again. "I understand your reasons to blame it on him, Skipper. Heck, I'd want to blame it on that madman myself. But we don't have enough evidence to prove that it's him. For all we know, The Aces might have just recruited someone like Kowalski."

Skipper opened his mouth to say something, but immediately shut it again. He took a deep breath to calm himself down. "You're right. I'm sorry, Tom. No jumping to conclusions. Got it."

Tom raised an eyebrow. "That's it? No argument, no nothing?" Skipper shrugged. "I'm tired."

Tom nodded carefully, still not completely convinced. "Alright then. If you're tired, why don't you just go ahead and take a rest? And I mean all of you, of course."

"Yes, Tom." They all said at the same time. And with that, they began to walk out the door one by one.

"Oh, and Skipper?" Tom said just as the leader Penguin was walking out. "When I said rest, I mean rest. Don't let me find you in the training room today." Skipper waved a hand without turning around and continued out the door.

Tom smiled when he was once again alone in his office. He looked down at his desk and traced the carving on it, thinking.

The door opened again. Tom didn't need to look up to know who it was. There were only two people that came into his office without knocking, and one of them was on a mission. "Hello, Eric."

"You know he's never going to listen to you, right?"

"Of course!" Tom laughed. "He's probably going to find another place to train or just disappear somewhere topside."

"Now doesn't that sound familiar?" Eric asked sarcastically. Tom chuckled. "Yeah, I know. Reminds me of me twenty-five years ago. But hey, if Dad took the time to try to speak some sense into me then, what's so wrong with me doing it now?"

"You mean besides the fact that Skipper's not your son?" Eric said with a roll of his eyes. "Absolutely nothing."

The Penguins didn't make it ten feet away from the office when Skipper stopped.

"Skipper? Are you okay?" Private asked worriedly. Skipper smirked and turned to the boy. "Why, I'm absolutely fine, Private. Now the question is, are you okay?"

"Eh?" Private blinked at this unexpected question. "You've been cradling that arm for quite a while now. What's wrong with it?" Skipper pointed at the arm that Private was carefully holding on to. Private shifted nervously and tried to hide his arm. "I-it's nothing, Skipper, I'm just, you know…picking up a new habit?"

"Right." Skipper said, every inch of that word dripping with sarcasm. "Rico!"

Private didn't even have time to blink when the bulky operative grabbed his wrist and pulled the arm up. Private winced at the strong grip as Rico rolled up his sleeve, revealing a long cut running up the arm.

Skipper drew in a sharp breath, which Private had long since realized was the leader's way of gasping. "Private, why didn't you tell us about this?"

"I didn't want to worry you…" He said uncertainly. "B-besides, it's already stopped bleeding. I figure it's nothing serious."

"Nothing serious? That gash is five inches long!" Skipper said.

"Actually, Skipper, it is only three inches long." Kowalski corrected helpfully. Skipper sent the strategist a glare that said "shut up now or else". Kowalski complied.

Turning his attention back on the boy, Skipper sternly said, "Private, I want you to go to the med bay. Now."

"Bu-"

"No buts. Now hop to it." Skipper said as he pushed the boy in the general direction of the med bay. But before Private could go, Kowalski suddenly cleared his throat. "Um…Skipper? I'm requesting permission to go with Private."

Skipper stared. "Kowalski, Private hurt his arm, not his legs. I'm pretty sure he can find the med bay without running into a wall." Skipper almost laughed when the taller operative gave him an almost pleading look. Realization dawned on Skipper and he smirked. "Oh, I guess it wouldn't hurt. Go right ahead, Kowalski."

"Thank you, Skipper." Kowalski said gratefully. He quickly placed a hand on Private's shoulder and guided the young Penguin away.

As the duo disappeared round the corner, Skipper gave an amused chuckle. "Look at him, Rico. Have you ever seen a man more in love?"

"D'awww." Rico replied with a smirk. Skipper smirked back, and they shared a high-five. "And he thinks we don't know. Seriously, how stupid does he think we are?"

"Really, Kowalski," Private protested. "You didn't have to come with me."

"Oh, I don't mind." Kowalski said quickly. A little too quick. Private thought about it for about two seconds before hitting his fist against his palm. "Oh, I get it! You want to see-"

He never finished the sentence, as Kowalski had clamped his hand onto his mouth, a blush starting to spread across his face. "Don't say it out loud!" He hissed in a panicked whisper. Private nodded to show he got the message before pushing the taller operative's hand away, thankful that he's able to breathe again.

"But, Kowalski," He asked confusedly once he caught his breath, "If you like her so much, why don't you just tell her?"

If possible, Kowalski's face went even redder. "It's…it's complicated." He said weakly as he turned to stare at the passing wall. Private looked at Kowalski's flustered face and giggled, ignoring the pain that was still on his arm. Kowalski cleared his throat, pushed up his glasses, and tried to maintain what little dignity he had left. "A-anyways, you'll understand as you grow older. Right now, we need to get that arm of yours treated. Wouldn't want it to get infected"

"Right." Private replied cheerfully, a teasing tone evident in his voice. Kowalski returned the tease by ruffling the shorter Penguin's hair.

Kowalski managed to suppress his blush as they neared the med bay. Taking a deep breath, he reached out to open the door.

He didn't get more than three inches closer before the door swung open and hit him square in the face.

"Ow!" He cried out, stumbling backwards. Private, being right behind him, hurriedly tried to support and steady the scientist. But Kowalski's weight proved to be too much for the boy, and they both tumbled to the floor.

Kowalski collected himself enough to look up through his fingers. A very surprised light-haired replica of Mason stared back at him. Kowalski groaned. "Phil…"

The other man looked at him guiltily before running through a series of hand signs. Kowalski stopped him at the twelfth. "Look, Phil, I don't understand sign language. Even if I did, you're going way too fast for anyone to understand." He rubbed at his nose. "I guess you're trying to apologize. I'm fine. You might have given me a broken nose, but I'm fine."

"A broken nose?" A new voice suddenly cut into what was starting to be a one-sided conversation. Kowalski felt his blush threatening to return as another person stepped out from behind Phil. Violet eyes met his blue ones as the person, now revealed to be a young woman, laughed lightheartedly while smoothing her white medical coat. "I've seen your nose survive worse than a swinging door, Kowalski. I'm sure it's fine." She finished with a soft pat on Kowalski's nose. The strategist blushed again, this time in embarrassment.

"Doris…" He said in a voice that was almost a whine. The blue-haired medic laughed again. "Well, if you're so worried, I'll take a look at it anyways. Oh, and you might want to get off poor Private."

In the Penguins' living quarters, Skipper leaned back in his chair. His mind was racing with what they had found out earlier.

It has to be him. He thought. As much as I hate to admit it, he's the only one I know that's better than Kowalski.

His fingers clasped themselves together as he brought them up to his mouth, a pose he often took when brooding. He had to find out more about The Aces. So far their only knowledge of the gang was that they've been breaking so many laws that you could fill two books with their crimes. But if that person was involved, then The Aces were definitely a lot more sinister than they appeared to be. It always had. If he could only get Tom to see that…

What would you have done, Johnson? He found himself asking. He quickly stopped himself before he could fall into the painful memories again.

He sighed. Then he almost jumped when a small explosion came from behind him. He turned and glared. "Rico. What did I say about indoor testing?"

Rico, who was sitting amid his array of weaponry, smiled sheepishly. "Sorry." Skipper looked at the small, smoking crater that now marred the floor and sighed again. "Just make sure you clean that before Private gets back."

Rico nodded. Skipper was about to return to his brooding when a strikingly familiar (and loud) voice could be heard out in the hallway. Skipper blanched. "No…they can't be back so soon! They only left a minute before we did!"

Rico got up, his weapons now safely hidden in his clothes, and opened the door to the hallway. He gave his leader a knowing look. Skipper returned the look with a grateful one and ran out the door. He had to get away before…he came.

He was about to round a corner when a blur of brown and gray invaded his vision. He stopped before he could ram into the upside-down face that was grinning at him, flashing its almost perfect teeth. Skipper cursed. Too late.

"Silly Penguin. Where do you think you're going?"

To be continued…

Okay, if you thought the one Kowalski was blushing so much about was Marlene, raise your hand. *All Marski fans raise hands* …Thought so. Sorry, the pairing here is Koris/Kowaris, whichever you prefer. For those of you worried about there being no Marlene, well, you can stop. Marlene will be in this story, but she'll be a little late.

Ah, the last part seems rushed. Honestly, I ran out of ideas for that scene. So it turned into that. I don't really like it myself.

Kudos to anyone who can guess who the mysterious that person is. It shouldn't be too hard.

Another thing. Tom and Eric are just names that I decided to use for my "chief" characters, and have nothing to do with Tom McGrath and Eric Darnell themselves. I considered Alice, but it didn't seem likely that Skipper would take orders from her, even if she was his superior. I even considered other animals in the zoo, but they didn't seem to fit, either. So in the end, I went with the directors' names. It just seemed better that way.

And now to prevent my Authoress' Note to become as long as the chapter itself, I'm going to shut up and go work on the next chapter, which should be out within two weeks. Hopefully.

~ruth~