Summary: Join the penguins as they face their greatest threat yet, The truth! What really happened to the infamous duo Manfredi and Johnson? Find out in this latest thriller where you will discover that horrifying secrets hide behind the most trusting of faces. Can our heroes survive the ultimate test of their brotherhood? Or will their team finally fall apart? (Sequel to: Penguins of Madagascar 2: Operation Blowhole)

Disclaimers: I do not own The Penguins of Madagascar

Author's Notes: Greetings readers and happy new year! Yes 2023 here we are, right out of the door with a new story, Penguins of Madagascar 3. I know, I know a lot of you hated the long wait for this installment but it's finally here! And yes I know the story title has changed from the original. In the beginning I was going to have the duo return to the zoo suddenly and slowly explain their backstory throughout, but during the planning process I decided that going back and forth from the present to the past might get complicated. So I decided to do the backstory first and then have the duo show up in present time. Currently I am planning for 10 chapters but that may change as the story progresses. I'm hoping for this to be one story but depending how it goes it might be a two parter.

My Goal is to keep what really happened somewhat of a mystery while answering a few questions that where presented to me in the reviews for Penguins of Madagascar 2: Operation Blowhole such as:

1. The Mr. Tux storyline

2. Where do all of Skipper's Aliases fit in

· Two-Bit Hood Jack the Knife

· International Play Bird Diego Garcia

· Wealthy Industrial Lincoln Douglas

3. Uncle Nigel and where he was when Private was abandon!

4. When the penguins meet Manfredi and Johnson

5. How much of the wild stories about their "deaths" are true?

6. And how do they end up in Seaville Aqua Fun Park

So yes this one maybe lengthier than the others. With that said, Thanks for reading and please enjoy.

Yours Truly, RoxieDivine

(Three Months after Operation Blowhole…)

[Skipper's POV]

Skipper's Log

I wish that I could say that things were better now…

They should be better now…. Right?

We had discovered the mad mammal's evil plot, we had tracked him down, and most importantly: We had stopped him. It should be over now, but it isn't. We have spent countless hours, hours that have bleed into weeks, and weeks that have seeped into months.

I want to believe that it was time well spent, but I feel like nothing has changed. My obsession for the master mind of Denmark has not lessen. If anything it has grown and it keeps growing with every passing day.

The only difference is I am no longer the only one who is fixated.

My brothers are now just as consumed as I am. We can not keep living this way, hours without sleep, dropping everything at the slightest possibility of the enemy showing their hand. It's driving us crazy, me most of all. I did this, I brought my existence in full view of a very powerful enemy, one that has followed me home. I know we can't keep going like this forever, but at the same time I know none of us will stop.

We can't stop, this monster wants to flood the entire world. I have no doubt that he will strike again, but where? That's the problem, we have no clue and if we don't think of something quick…we can't keep doing the same thing.

All day long we play zoo and all night we search and hunt down our enemy. As much as it pains me to say it we have to change tactics. I don't think…no I know my brothers will not like this idea, but it is the only option we have yet to try…

Skipper's Log-END

[3rd Person POV]

Skipper presses the stop button on his cassette player and fights back a yawn.

The morning wakeup call is blaring from the lair's speaker, coaxing his brothers out of what little sleep they had managed.

Rico is the first to join him at the table and presents him with a cup of joe.

"Thanks." Skipper tried to sound upbeat, but his voice lacks luster.

Rico grunts a morning greeting.

Kowalski is next to drag himself over, his overall demeanor reminds Skipper of a Zombie. The scientist had been spending the past few months trying to bring since to the madness. He was so sure that he could find some sort of design. That if he listed out all the events that led to their encounter with Blowhole that would find a pattern. A model they could use, so that when similar events happened they could find the dolphin and stop him once and for all.

It was no use, Blowhole left nothing to trace and with no, trace no pattern could be formulated.

It was a dead end, just as all their plans had been before.

Skipper wondered if this plan would be any different.

He knew somebody had to know the comings and goings of their enemy. He also knows that those people were most likely criminals. This fact alone was why he hesitated, were they ready for what he had to propose. He looks to Rico, his brother was strong, and could handle his own. Still he was a loose cannon who needed a firm hand to real him in.

Skipper shifts his focus to Kowalski, again he knows the scientist is capable. Regardless, he also had a bad tendency to over think things. Then there was Private, the youngest brother was practically sleepwalking to the table.

"Morning Skipper." He mumbles and nearly trips over his chair before he manages to sit down. Skipper knew Private had potential, he showed as much when they face Dave. However, they had also been so close to losing him. Should he risk it? Should he even mention this crazy plan that had been haunting his mind for the past week?

"Well don't leave us in suspense." Kowalski decided to jump right into it. It was obvious that his eldest brother had been raging an internal war. They might as well cut to the chase, but part of him feared he already knew what it was. Skipper was wearing the same look on his face after Classified had asked him to leave, alone…

Skipper took a deep breath; his brothers were fully focused on him now. This was it; it was time to put all the cards on the table. What he was about to propose would test them in ways they had never been tested before. He knew this because he had just done it not too long ago himself and he had failed miserably. Would they fair better now?

He hoped so, it was the only option left.

"We can't keep going like this…" He finally began.

Kowalski nodded. "Any suggestions?"

"Blowhole had resources, education, and the respect of an army. That takes connections, money, networking." Skipper explained.

Kowalski nodded; this too had crossed his mind. He knew just as much as Skipper that there was an underground network of criminals in the animal kingdom. But said criminals lived under an unwritten code. No one sold each other out and no one would talk to good doers like them.

Skipper nodded as if he could read his mind. He had came to the same conclusion. "They won't talk to suits like us."

"Are you suggesting we go undercover?" Kowalski asked.

"Would that even work?" Private asked, surprising them all. "I mean we've taken down two major villains on a large scale. Sure Northwind covered up the Dave incident, but villains talk…"

Skipper couldn't help the sense of pride that filled him. He had thought the same thing when Classified had approached him. Northwind had protected them last time, but nothing was protecting them now, no doubt Blowhole would warn his connections of the new threat.

"Which is why we can not approach this as a group." Skipper finally dropped the bomb shell.

"You mean go undercover; Each of us? Alone!" Private's voice was a panicked shrill, reminding Skipper just how green his brothers were. Only Skipper alone had gone on a solo mission, no he shakes off the doubt. He could not doubt them, or they would doubt themselves.

"I have studied what we know about the criminal underworld." Skipper assured them. "And I have found a niche that each of us can blend in seamlessly." That was a lie, he had only found places for himself, Rico, and Kowalski. Private however, had never showed any possibility of fitting in with criminals. This of course wouldn't normally be an issue but when trying to blend in with the worse of the worse. Well, Skipper just couldn't see it in him.

Skipper pulls out some files he had put together and slides one to his weapons expert.

"Rico you are a new weapons dealer, who hopes to make it big time in the underworld. Your job is to blend in with other smugglers and try to scope out Blowholes suppliers. If we can find them, we maybe able to find Blowhole."

Rico nods and looks through the file, there are pictures of suspected hot spots for smugglers. Of course the information had been swiped from the Northwind databases. A task that had been easily done.

Skipper couldn't help but cringe at that. They had visited the Northwind headquarters in hopes of getting some help from their old friends. Surely they had resources, something they could use to track and find Blowhole. But the base was nearly empty, most of the equipment gone and the rest laid in broken pieces.

It was obvious that Eva's stunt had run them out of business, with every agent known they had to close up shop and put their people and their families in safe houses. Northwind was dead, but the trip wasn't a total lost. Kowalski was able to recover the pieces of a few hard drives and managed to salvage some of their data.

This information was what led Skipper to the plan he had now.

Information of the criminal underworld, supply lines, suspected informants, and known crime lords.

It was a solid plan on paper, sometimes the only way to find a criminal was to access their world. The real question was could they pull it off? Could they overlook a world of criminals in hopes of finding just one?!

"Kowalski as a scientist you'll be able to worm your way right into the community Blowhole is most likely already apart of." Skipper passes the next folder to his strategist.

"You want me to pose as a mad scientist?" Kowalski asked.

"You nerdy types like to brag about your accomplishments." Skipper reasoned. "And Blowhole proved to us during our encounters that he likes to do just that."

Kowalski supposed it couldn't hurt, after all Private was right. Villains talked to each other, and scientist did like to compete with one another. No doubt they would rub their exploits in each other's faces. He just needed to find out how, his guess was some dark web connection, and his file supported the theory. "And you?"

"I'm going to focus my efforts on the crime bosses." Skipper answered. "Rub elbows with them. Conquest is a game and there is no way they are unaware of a new player as resourceful as Blowhole."

"And me Skipper?" Private asked hopefully, even though he could tell it was hopeless. His commander only had three folders.

"He can join me." Kowalski said swiftly. "Evil scientist always have an assistant."

Before Dave, Private would just nod his agreement, but now he stood his ground. "I can do more Skipper." He insisted. He had proved as much; he had saved his brothers and led them to victory. He was ready to take on just as much responsibility as the rest of them.

"Private I…" Skipper begins.

"Uh guys?" Marlene asked as she peaks in from the top hatch.

"Seriously does secret base of operations mean anything to you?" Skipper asked.

"Yeah if it's so secret then why is someone here asking about you?" Marlene asked.

"What?" Skipper was on high alert now. "Whose asking about us."

"He's up here." Marlene whispered. "He has some picture of you guys, and he keeps pointing at Private."

"Me?" Private shivers despite himself. "What would a complete stranger want with me?"

"Well that's the funny part." Marlene said, but her tone detects no laughter. If anything she sounds creeped out. "He says he's your uncle."

"My uncle?" Private is beyond disbelief.

"Preposterous." Skipper snapped, stepping in front of Private.

"Actually it could be possible." Kowalski reasoned. "We did find him abandon as an egg. The odds his parents were alive…. slim." He admitted giving the younger penguin an apologetic look. "But an Uncle, looking for a long-lost nephew…it's plausible."

"Right, right and him showing up months after we've face are great and most dangerous foe is just a coincidence."

"Fair point…" Kowalski agreed.

"Look guys I don't care what or who you think he is, he wouldn't leave me alone until I took him over here and he is not leaving until you speak with him." Marlene whispered urgently. "Please, this guy isn't taking no for an answer."

"At ease Marlene, we'll take the spy off your hands." Skipper tells her as they start to climb the ladder to join her top side.

"Yeah I doubt he's a spy." She admitted. "And trust me he is Private's uncle."

"How can you tell?" Skipper asked.

"Oh I don't know call it a hunch." Marlene said as she gesture to her left.

The brothers turn to see the visitor in question. He's an older penguin with unfocused eyes and messy spikey feathers. He's currently pouring cups of tea that he has set out on a makeshift table. Upon further examination Private notices it's a suitcase with a tablecloth draped over it.

There eyes meet and the older penguin looks relieved.

"I can't believe it." He has a heavy British accent, and he puts down his tea pot with shaking hands. "It really is you…after all this time…I was starting to lose hope…" He walks over quickly, overcome by joy.

No one moves to stop him, too stunned by the obvious resemblance.

The stranger embraces Private, and for a moment he feels a sense of belonging. Something deep in his gut just knew this person was sincere.

"Oh Sammy I thought I lost you."

Private stiffens. "Sammy?" He asked. All feelings of belonging washed away. It felt like he had been doused with a bucket of cold water. "Sorry I think you have me mixed up with someone else. My names not Sammy, it's Private."

"Private? Are you sure, you look just like my brother Samuel. Does that name ring a bell to you."

"Look Mr. We don't know who you are…" Skipper began pushing himself in between Private and the stranger. He had been thrown off in the beginning, because of the strange similarities, but now the spell was lifted.

"The names Nigel, Nigel Fishy, brother of Samuel Fishy." He looks to Private hopefully.

"I'm sorry, I really am." Private said. "But I don't know that name."

"Really, well I suppose,…no." Nigel shook his head. "The likeness is uncanny."

"Look I'm sure you're a nice guy." Skipper said, not sounding convinced at all. "But we found Private all alone."

"Was it a little over ten years ago?" Nigel asked.

Private felt his breath caught, they all did. His brothers had found him just moments before he was born. And he had just celebrated his 10th birthday four months ago. Was it possible, could this really be some long lost relative, one who has been looking for him this whole time.

"Please, at least hear me out." Nigel begged. "I've come a long way…I've been searching for so long."

The guy looked desperate, and Private felt his heart bleed out for him. Still part of him didn't want to believe it. He already had a home and a family who loved him, and this stranger was just coming in and trying to insert himself. It's a silly thought, but Private feels guilty for being happy to see him. For being hopeful that there was some truth in his claims. After all his brothers had done for him, how could he betray them in such away. And yet, the other part was wrapped up in the what ifs.

What if he was his uncle? What if he knew what happened to his parents? What if he knew why he was all alone in the Artic? Private never let it show, but sometimes he would wonder. He always felt guilty when he did, but the older he got the harder it became. He would look at his brothers, and it was obvious they were brothers. They looked similar, talked the same, Private was the one who didn't belong. Sometimes he would look in the mirror and wonder who's face was looking back at him. Did his parents leave him by choice, did they not want him? This could be the end of all his questions.

"Well I guess it wouldn't hurt to hear him out." Private relented.

"We will do no such thing-" Skipper began.

"Skipper." Kowalski shushed him. "This is about Private."

"He is not his family, we are!" Skipper snapped.

"We found him alone in the ice, if it were you, wouldn't you want to know why?" Kowalski lectured.

Skipper looks to Private hopefully and sees that he too looks hopeful.

"Skipper please, I…I have to know." Private whispered.

It pained him to see him this way, but it pained him even more to give in. "Okay." He said looking to Nigel. "Tell us what you know."

End Notes

So some fun facts about this chapter. According to the GBA Game, Madagascar: Operation Penguin, Sam Fishy is the name of Private's biological father. Who was mentioned by Private who says, Sam once snuck into the CIA and stole all their ice creams.

Nothing else is known about him or Private's mother who is never named. With that said I had to make up the rest of Private's origin story which will be explained in the next chapter. So stay tuned and happy New Year's everyone!