Secret Research Facility

Mii city of Nintendopolis

A lone cardboard box lay dormant in one of the facility's hallways. Two patrolling Primids had just walked by and noticed the box. Oddly, they weren't expecting a delivery. One of them nudged the box with the butt of its laser rifle, but nothing happened. It turned to its companion, who shrugged, dismissing it as nothing. The two then continued on with their patrol, reporting nothing suspicious in the sector.

But the box proved to be the only suspicious thing.

The box was hoisted up and discarded, revealing Snake, an elite soldier trained in stealth tactics, underneath. He keyed into his earpiece. "Alright HQ, I'm in. Those creeps didn't suspect a thing."

Snake carefully traversed through the dark corridors, keeping a watchful eye out. "Walls must be shielded. Clever to protect themselves from an attack."
"All this time and right under the citizens' noses, huh?"

Snake whirled around and pointed his pistol in the direction the voice came from-behind him. There, a red wolf with combat boots, gloves and glasses with a microphone stood leaning against the wall with his arms crossed.

"I could have killed you!" Snake hissed as he lowered his weapon. The wolf just chuckled. "A being that could bend reality with a gem and a mad doctor with an army of robots tried. Anyway, HQ figured you could use some help, so they sent me."

"I told them I don't need help." Snake replied in an annoyed tone. "I'll get the job done faster alone." "Alright, totally understand. I'll just, uh…"

Snake noticed something behind them. Two lone Primids had seen them and were moving in fast, beam swords drawn. "…leave you guys to it then." The wolf finished as he drew out a red flamethrower from his back.

Since there were only two of them, the Primids were quickly dealt with just a few flame bursts and pistol shots. Snake seemed curious about the newcomer. "Judging from the looks of you, you're friends with the hedgehog. You got a name, kid?"

"It's, uh, classified. But I do have a codename. Avatar. You must be Snake." The red wolf held out his hand for a handshake, but Snake didn't take it. Instead, he turned down the hallway and continued his path. Avatar just shrugged and followed him.

Soon after, the duo stopped in front of a large steel door. "Hold on." Avatar said, holding up a hand. "I'm picking something else from behind there. Allow me." We took out his Burst Wispon and fired at the door control panel, destroying it in flames and causing the door to slide open…

…causing a figure in green clothing to collapse clumsily onto the floor in front of them, as if he had been leaning against it. The figure got up, dusted himself off and adjusted his cap with a green "L" on it. As soon as he noticed the other two, he stood up straight.

"Aha!" Avatar shouted, pointing at him. "So you're the guy who's been tailing me for the past hour! The second half of the brotherly duo!" Luigi just shrugged in defeat. "You're not even supposed to be here, are you?" Snake asked, now more annoyed that he had two guys to deal with. Luigi looked at Snake and began to explain, but all that came out was a series of incomprehensible babbles.

"Hang on, I think I can translate." Avatar interrupted. "Apparently, he's been hanging out in the city for a while and he heard that strange stuff was going on. Recently, he noticed that some 'purple space aliens' had just attacked a town five miles away from here. Their weapons and equipment seemed to originate from this location, so he drove his racing bike over here to investigate."

"I don't have time to play nursemaid for you two." Snake grumbled. "Hey! I'm not sure if you know, but Luigi here's covered haunted mansions!" Snake sighed. "Fine, but one: Stay out of my way, and two: Don't. Touch. Anything. Got it?"

Both Avatar and Luigi nodded. With that out of the way, the trio continued deeper into the facility. After a few minutes, Luigi caught wind of something and ran down another hallway. Snake and Avatar followed to see Luigi with his jaw dropped. The other two followed his gaze… to see various wild Pokémon in containment pods surrounded by purple tubes.

Luigi ran by every pod, staring at the creatures inside, even knocking on a few, but with no response from the test subject. "Squirtles, Charizards, Raichus… so many Pokémon." Avatar whispered. "Based on what the masked swordsman told me, they're planning on the corrupting them with some kind of serum. Making them into weapons that serve the Subspace Army." Snake explained.

Suddenly, Luigi yelled from up ahead. Snake and Avatar ran up to the very front to see a non-Pokémon in the pod… Wario, biker's jacket and all. "Oh no…" Luigi whimpered. "We've got to get him out of there, now!" Avatar shouted. But before anyone could do a thing, the microgame maker stirred from inside the pod… and opened his eyes.

With a loud crash, the pod shattered and Luigi was almost swept away from the water. Wario jumped out and landed with fists balled. He was perfectly fine with no corruption symptoms in sight, but he was visibly upset.

"You chumps just made the biggest mistakes of your lives!" Wario yelled as he pounced at the trio. Luigi tried to run, but Wario grabbed him by the torso and slammed him to the ground like a wrestler. Avatar jumped in and landed a punch-kick combo to Wario's side and head before he knocked the wolf back. Snake had to step in, so he kneed Wario in the chin and punched him hard, making him collapse to the floor.

"Ugh, my head." Wario groaned. "Did I have too many garlics?" Sitting up and shaking his head, he noticed a particular figure. "You?" he asked, pointing to Luigi. "What the heck are you doing here? Where's your stupid brother?" Luigi could only scratch his head.

"Long story. Can you remember what happened?" Avatar asked him. "Eh, not much. I was going for a joyride with my bike through the streets of Diamond City when suddenly I saw a U.F.O. or something! Next thing I know, here I am, pummeling the snot out of Green Stache! Hey, where the heck am I, anyway?" Luigi just rubbed the spot where Wario had slammed him, as if this wasn't the first time he had dealt with his brother's rival.

"Quiet, all of you!" Snake ordered. "I hear something." Everyone was silent, and they heard it too. Voices.

"The specimen is not progressing as Command has anticipated. We require more time." That voice belonged to a Subspace clone of Dr. Robotnik, better known as Sonic's old enemy, Eggman. Beside him stood a Subspace clone of Dr. Wily, Mega Man's foe. He, too, looked annoyed.

"There is no more time, doctors." A new voice spoke. This one was a Subspace clone of Ganondorf, who seemed more sinister than his counterpart. "Perhaps your arrogance outstrips your intellects, even for duplicates of your counterparts."

"What?!" False Eggman roared. "Our intellects combined is unmatched! That is why we are the best scientists in the Subspace Army! The Army shall have their new recruits, along with absorbing the power of the Stone fragment to strengthen our growing ranks! Now go! We must work!"

"Do not fail me or the master, scientists." False Ganondorf threatened before a purple dimensional portal opened, which he stepped through before vanishing.

"What's wrong, copies? Having trouble with your lab partner?" Avatar quipped. "Intruders!" False Wily shouted. "Release the test subjects! Now!" False Eggman slammed his fist down on a button, and one by one, the pods containing the corrupted Pokémon shattered, freeing the enslaved creatures. They noticed Snake, Avatar, Luigi and Wario and instantly charged towards them.

Luigi ducked as a Charizard dove at him, Snake fired his rocket launcher at a Blastoise, Avatar kicked away a Raichu, and Wario punched some smaller Pokémon away. "There's…just…too…many…of them!" Avatar grunted after he kept a Greninja away with a flame wall. "Cover me!" Snake yelled. "I'm going for the Stone piece!" As he made a break for the fragment, which was connected up to a machine, Wario belly-slammed an Axew while Luigi threw a green fireball at a Lucario, who dodged it and slammed Luigi into one of the pods. Avatar had to save him by jump-kicking the Lucario in the head.

"Stop them, you fools!" False Eggman shouted. A Pikachu leapt at Snake with electricity around its body, but Avatar grappled it and threw it at a bunch of corrupted Pokémon, electrocuting them all. With the other three keeping the incoming wave busy, Snake deactivated the machine and snatched the piece from it, causing the rest of the equipment to malfunction. "Nooooo!" both scientists screamed as lightning from the destroyed equipment shocked them and making them dissolve into Shadow Bugs.

"Shut this down, now!" Snake yelled, pointing to a console powering up a purple dimensional rift. Luigi rushed to it and began bashing it with his hammer (also whacking a Ditto copying him with it when it jumped at him). However, his efforts only made a small dent in it.

The whole facility started to shake and the portal shuddered. Something was forcing its way through. "Oh no." Avatar whispered as the corrupted Pokémon around him stopped fighting to see what was coming out. "We gotta go. We gotta go now!" Snake tucked the Stone fragment away as the four of them made a beeline for the nearest exit as the thing emerging from the portal let out a massive bellow…