This idea popped into my head after watching MatPat from Game Theory post a video on YouTube that theorized about the true nature of the Toads. Whether or not it's true doesn't matter really, it was an awesome idea anyways. This fanfiction is a direct spawn of that.

Now, for reference, I am drawing heavily on Super Mario Advance 4: Super Mario Brothers 3 (SMA4:SMB3) for this, namely for the locations and names of the Koopa Kids. Of course, Bowser Jr has been worked in even though he's not actually a part of that game, but this is not game accurate in a lot of accounts.

I will explain more of my reasoning at the end. For now, Enjoy!

~FS

A Tale Of Two Kingdoms

"Honestly you fool," grumbled the eldest Koopaling as he and the Head Guard moved down the halls, "Why are your guards such idjits? Surely you know that those Red Guards of yours are useless."

The Head Guard sighed, "Well Lord Ludwig, that is rather the point. The grunt guards are merely to be an obstacle that will warn us of enemy approach. Then we can send Kamek, Boo, and Dry Bone Divisions of the Guard in to take down the enemy."

Ludwig Von Koopa sighed as he twirled his wand, "I guess that makes sense Ryker. At least we aren't having any further troubles right now beyond their uselessness. The bases we have begun to set up in the Pipe Maze are going smoothly all things considered."

Head Guard Ryker nodded, "I'm actually a bit surprised that the local ruler there is cooperating right now. What with all the other lands so infatuated with the Mushroom Kingdom." Ludwig snorted but couldn't help but agree mentally.

"It is rather strange," Ludwig scratched the back of his head, musing to himself, "Perhaps there is something foul afoot that we should be worried about..." Laughter came from their right and the two turned to look down the hallway.

Walking up to them was a Koopaling with blue shiny hair and a goofy grin, "You're always worried about nothin' old fart. There isn't any problem. Those Shrooms are a bunch of wusses, they're not planning anything at all."

Ludwig scowled at the youngest of the Koopalings, "Watch that mouth of yours Larry Koopa! Need I remind you King Bowser has put me in charge of you and any discipline that may entail?" An evil glint appeared in the eldest's eyes, "Or should I demonstrate that little fact out here in the open."

Larry winced and shook his head, "No sir, that's not necessary." The youngest shrugged, "Seriously though, between the pacifist Goombas and those damn silly Toads, there's nothing to worry about." Ludwig conceded the point.

Ryker looked at the Koopaling curiously, "I don't think we've ever met Lord Koopa. May I have the honor of introductions?" Larry looked at him a bit surprised for a moment before laughing once again, shaking his head a bit.

"Sorry forgot about how everyone here in the Palace talks. High Court and etiquette and all the crap." Larry grinned at the Guard and Ryker nodded, "I'm Larry Koopa, Lord Larry Koopa technically, youngest of the Koopalings."

Ryker's eyebrow arched, "Youngest? I thought that honor went to Prince Bowser Jr.?" At Larry's scowl he quickly continued, "I of course meant no offense Lord Koopa, I merely knew not how to voice my surprise." Larry waved off his comment.

"It's fine, I just don't like the brat," Ludwig started laughing at this point, Larry glaring at him, "Yeah laugh it up older bro, I realize I sound like you talking about me. But seriously, why does that little bitch get to be the heir? I think he blackmailed Daddy-dearest or something like that!"

A small chuckle was heard behind Larry and the two Koopalings stiffed. Ryker dropped to one knee, "Crown Prince Bowser Jr!" Larry turned around to the grinning face of his possibly younger sibling and mentally groaned at the coldness in his eyes. Speak of the fucker and he appears.

The Heir twirled his staff in one hand, "Did you have something to say to my face dearest brother?" Larry said nothing, not wanting to get in any worse trouble. Bowser Jr. grinned, "Kukuku, very well. I will move on then. Oh Ludwig? Discipline the lad will you."

Larry fumed as Bowser Jr walked away whistling. Ludwig sighed as Ryker looked at Larry sympathetically; he wouldn't dare to say it out loud but the Crown Prince was a bit of a spoiled brat. He was nothing like his father, who was ruthless yet just.

"Anyways... after that little episode, perhaps we should finish introductions," Ludwig said, trying to get back on the topic they were on before their brother had shown up. Larry noded, before looking over at Ryker.

"You said we haven't met before? I guess that means you got promoted after I left a year or so ago to look over our troops in Sky World. Our Lakitus over there have been training some really nifty Para-Beetles and Para-Troopers," Larry said absentmindedly before focusing, "So then, who are you?"

Ryker straightened and saluted, "Head Guard, Commander Ryker, MQD, one of the fire Bros." Larry whistled, grinning before clapping the Guard on the back.

"MQD? The Military Quarantine Division? Damn dude, you must be pretty good- makes sense though. They don't let random Red Guards become MQD or Head Guard." Ryker bowed his head at the compliment, humbly accepting it.

A whooshing sound was heard as a Lakitu zoomed down the hall, stopping in front of the trio. They all looked at him and he quickly rushed out, "King Bowser would like to see Lord Ludwig, Lord Larry, and Commander Ryker in the Council Room immediately."

They nodded their consent and the Lakitu zoomed off yet again. Ludwig mused, "Something is up! I knew it! What could it be..." Larry facepalmed and muttered something about Ludwig being an 'old fart'. He shut up as Ludwig sent him a withering glare.

"Maybe it's about how all the Toads suddenly have these weird hats on en mass. Or the fact they seem unusually loyal to the Monarchy in the Mushroom Kingdom. Or perhaps..." Ludwig continued to speculate the entire way as Larry and Ryker engaged in conversation.

As they entered the Council Room, the deep baritone rumbles of the King could be heard talking to one of his other sons, "Lemmy... I understand that you're happy to find such a friend, but I'd feel better if you didn't hang around him to much."

The long table currently was occupied by four of the Koopas; Wendy at her seat, Roy in his, while Lemmy was up at the head of the table talking with their Father, King Bowser. Larrry went to his seat, and Ryker to his. Ludwig slowly approached his seat on the right of his Father, as he was second-in-command.

Bowser sighed as Ludwig slid into his seat, "Lemmy, go take your seat. We will talk more about this later." Sadness filled Lemmy's eyes but he did as his Father asked. Ludwig looked quizzically at Bowser.

Softly, Bowser explained, "Lemmy has found a human friend who knows magic that lets him change into a Koopa believe it or not. They seem to be bonding well but..." Bowser sighed and continued, "this isn't the first case of this happening son, transformation is a truly ancient magic. My own brother knew someone similar."

Massaging his temples, he continued, "My brother fell for the human women and it led to his death at the hands of her accomplices. I just don't want that to happen to Lemmy." Ludwig nodded, watching his siblings as they talked, "Granted, these are two both males, but such relationships are not uncommon these days, even amongst our Kingdom."

Ludwig thought for a moment before speaking, "I believe you just need to trust Lemmy Father. If that is the way his preferences lay, treat him the way we treat all of those like him; with respect, understanding, and patience. He does not want to disappoint you, and your duty is to be just as King."

Bowser let a small smile creep on his face, "Wise advice son. Thank you, I am grateful for your council." Ludwig bowed his head, smiling. His Father was a good ruler, ready to take advice. They were lucky to have him.

"Good evening loyal peasants." Ludwig mentally groaned as Bowser Jr entered the Council Room. Every King had a flaw though and Bowser's had been Bowser Jr. Why their Father paid such special attention to him no one knew, but knowing the King there was a reason.

Still, Ludwig had tried to tell his Father to let him have the same control over Bowser Jr as the rest of the Koopalings; he had trained them all while their Father was busy and they were all good citizens, if somewhat eccentric. But Bowser did nothing. It was the one thing that his Father did that frustrated Ludwig.

The rest of the Council Room eventually filled and roll was called. All the Koopalings were there; Larry, Morton Jr, Wendy, Iggy, Roy, Lemmy, and himself, Ludwig. Also present was Head Guard Ryker, Head Mage Kamaluk, Head Engineer Bullwinkle, and Head General Hammerfist. And of course, Crown Prince Bowser Jr and King Bowser.

"Now, I have called you all together because of a problem that has been brought to my attention." Bowser waved to a Red Guard, who opened the door allowing an old Goomba to enter. The room buzzed at the sight of the citizen of the Mushroom Kingdom. Ludwig's eyes narrowed and he called for silence.

Bowser thanked his son before motioning to the old Goomba, "Now, Chief Gordon, please tell the Council what is the reason for your visit here." The Goomba nodded, silently composing himself before speaking.

"Council, I come to you on behalf of the Six Great Goomba Tribes. We have fled the Mushrooom Kingdom and have come for your aid." Gasps went around the table at this; why had the Goombas fled? "We left because a malady has fallen on the land, and we feared for our lives."

Kamaluk leaned forward, eyes hidden behind his spectacles, "Kukukuku, now what malady is that? And why is your own Kingdom ill-prepared to handle it?" The Goomba sighed before elaborating.

"Surely you have heard reports of the Toads' 'hats'?" Ludwig sent a victorious smile at Larrry who sighed in defeat. "They are not hats at all. They cannot be removed. They are fungal growths from what we can tell, and they have infected nearly every Toad."

Shock gripped the table and everyone began talking at once; after a moment, Bowser roared, "ORDER! I will have order at this council!" Everyone quieted down as Bowser addressed the Goomba Chief himself, "Who else has been infected?"

The Goomba thought it over, "I do not know about after we have left, but only the Toads have been affected as of now. The Princess and most other species are still perfectly healthy. But this malady..."

Everyone was quiet as the Goomba shuddered, "It takes over their minds. The Toads, once divided, are now united to the point where it's nearly impossible to tell them apart if not for their colored clothes. Though they are for now still weak and passive, I fear for the Kingdom. We all do."

Silence reigned. "We seek refuge and help. Nothing more." Ludwig looked over to his Father, who appeared to be mulling the situation over in his mind.

"You all may live in our country, as long as it takes for us to rid the Mushroom Kingdom of this menace." This drew everyone's attention; especially Bowser Jr's.

"But Daddy!" Everyone, save the King, winced as the Crown prince began to talk, "Why should we help the Mushroom Kingdom? Leave them! They are our rivals! What good will come of helping them."

Ludwig laughs at this statement, drawing Bowser's eyes. Ludwig quickly explained his reaction, "Leaving a parasitic organism thriving in the Mushroom Kingdom? I doubt it will collapse the Kingdom, and even if it did, the malady would spread here. Besides, whether or not we would normally wish the Mushroom Kingdom to become a lesser power," Ludwig looked into his Father's eyes, "Is it just to commend another Kingdom to death due to our interests?"

Bowser thoughtfully considered what his son had said; Ludwig pressed his advantage, "I would also suggest we extract Princess Peach from the Kingdom and quaratine her in the Castle."

Ryker nodded farther down the table, "That will thus keep the Bloodline of the Mushroom Kingdom's royal family intact. But surely these now infested Toads will retaliate. We cannot let the world be overrun by them if we strike against them. Perhaps we should bring more lands under our control until these Toads are freed of the parasite."

Murmurs of agreement spread through the table, though Bowser Jr quietly simmered in anger. The King nodded his head, "An excellent idea Ludwig and Ryker. I also know some ancient magick to transform creatures. I should be able to transform some of the infected Toads into inanimate objects, like bricks, or perhaps Horsetail grass."

Iggy nodded, "A natural fungus repellent." Everyone looked at him. He muttered in indignation, "I know things. I use it all the time over in the Pipe Maze. Stupid plant life is everywhere."

Bowser laughed, "Indeed Son. I will do this to keep the parasites from naturally spreading. They will have to fight us to expand." Bowser looked across the table. "I will assign each of you Koopalings an area to take control of and lock down."

Before Bowser did so, the Goomba Chief spoke up, "If it would please His Majesty, our men would like to help in any efforts to retake the homeland. They pledge their support so we can stop the menace."

The King nodded his approval, "Excellent. You will join my men then. Now, assignments. Ludwig," The King's second in command looked at his Father, "I want you to head to the Pipe Maze. It is the closest to our Kingdom. I need you in the back commanding our forward forces."

Ludwig nodded and Bowser continued, "Lemmy... I know you wanted to pursue your craft as a performer, but I need you to head to Iced Land and take control." Lemmy's shoulders slumped but he agreed.

Bowser looked at him sadly before an idea popped into his head, "You may however take your friend if you desire to." Lemmy's head snapped up and locked eyes with his Father; a grin spread over his face.

The King returned the smile before continuing, "Roy, head to The Sky and take command there. Larry can tell you about the advances our troops ave made there. Iggy, head to the Land Of Giants. Consult with Ludwig about our current positions."

"Wendy, head to Big Island. Morton, head to Desert Hill. Now Larry," The youngest's attention focused on his Father, "I want you to head to Grass Land. After your ship breaks into the castle and gets Princess Peach."

Larry straightened and nodded, determination in his eyes, "I won't let you down Father." Bowser nodded, trusting his youngest. They all had to grow up at some point after all.

"When you capture her, head to Grass Land and bunker down for immediate retaliation. Send her to Morton in a smaller ship. Do this relay across each land, that way any force attempting to follow will take a path through each of our outposts," Bowser said.

The King turned to his Heads, "I want our men ready as soon as possible. I want our fleets firing at full capacity, with every soldier of ours on alert." Bowser stood, fire in his eyes, "This is our most important war to date. We cannot let this Parasite take root in a fellow Kingdom so close."

The Koopa King sighed, "It's us or them everyone. Maybe they won't kill us today, but one day, they will infect us all or wipe us out." Bowser locked eyes with each of them and Ludwig felt his pulse quicken in excitement.

"We go to war. For ourselves, our allies, and the world."

Hope you all liked my take on what could actually be happening in the storyline!

Now, some explanations. The Red Guard are Red Koopa Troopas. The term "Koopa Troopa" is a Mushrom Kingdom term derived from the fact they work for the Koopas. It is not what I believe they would call themselves (mainly cause it sounds a bit silly).

As for nice and just Bowser, let me explain. We have seen he cares for his subjects across the games- but like every ruler in war has to scarifice them in battle to win. In this reality, the repeated wars are because they have to drive out the Toads, or die anyways.

Also, he totally seems like a family man because during certain games we've seen times he's actually had semi-heart to heart, non-violent conversations with, at least, Bowser Jr (ending of Super Mario Sunshine comes to mind). Also, Bowser Jr constantly brought him back to life in the New Super Mario Brothers game for the DS. Why do that if you hate the old man?

And while no where in the manual does the game (SMA4:SMB3) say anything about the Koopa Kids (or as they call them, Koopalings) being Bowser's kids, he's literally the only other Koopa we've seen (or that I know of at least). Who else could they come from?

Additionally, why set it up so Lemmy might be bi/gay?Simple; to drive home the fact Bowser could actually be a nice guy, and that he'd be looking out for his subjects, especially his kids. He does, or at least can, have depth, he's not (at least in this world) a power-driven maniac, unlike Bowser Jr.

Speaking of Bowser Jr being a spoiled brat, well, it suits him in all honesty. Heck, New Super Mario Brothers for the Wii U (If I remember which game it was correctly) was started because Bowser Jr gets the Koopa Kids to help him kidnap Peach. Inside a cake. Because he wants her for some reason. And in the previous game, Bowser Jr also kidnaps the Princess. It's not even Bowser's fault at this point, he just tries to protect his son from Mario. Like any caring Father would.

Basically, this whole fic is a "What if" Bowser wasn't straight up evil and there was a reason he kidnapped the Princess. It is intended to be a one-shot, but I can easily make it into a series if you all would like. Review and let me know how I did. Thanks!

PS: If you want to write a crazy rant or comment about how I haven't updated any other stories, I'm sorry. I've been trying to devote what little time I have to my own book and that's cut down on both my time for my other series and my inspiration for their chapters. I have most of a second chapter of Armageddon ready (finally) and then I'll try my best to get my other stories covered. Thanks for your patience!