Far outside the Yggdrasil, underneath the Legacy's shadow as it landed on the boarding platform, another strange warrior stood outside the gates. He was holding a sword similar to Lucina's Falchion, and he was wearing a shoulder plate on his left. He had blue hair, and he had the mark of the Naga on his right shoulder. His silver cape flowed behind him as he looked up, watching as Rathalos crawled on the surface of the ship, trying to claw through and attack any intruders inside.
"Hopefully my daughter isn't in that ship," the warrior said. "The least I could do is make sure she's okay, even if she knows how to defend herself from the moves of the Hero King…" Suddenly, he heard a hovercraft zooming right into his direction. The hovercraft had a yellow-and-green paint on its plate, and the back was filled with golden-skinned bananas marked with the Kong symbol in red. Two of a species of crocodile-like creatures were on each side, one green and the other blue. Driving the truck was a large, plump, brass-bellied reptilian king with red eyes and a loud laugh.
"With the Kongs gone to defend their Golden Banana horde, I can have all their delicious fruit to myself!" the crocodile king laughed. "Powering my ultimate weapon, these tasty treats will be the power of a lifeti- Whoa, whoa, whoa!" The crocodile king noticed the blue-haired warrior right in front of him, and he tried stepping on the brakes as his two minions held onto the hovertruck's sides. There was no time to stop the collision as a big whack from the hovertruck sent the two warriors flying. A brief explosion took place, and as the blue-haired warrior got up, he saw the crocodile king looking down upon him, furious.
"How dare you stop King K. Rool as he tries to escape with the one thing to destroy Kong Island…" the crocodile king growled.
"Stop you?" the blue-haired warrior asked. "My fellow comrade, I believe those bananas aren't technically yours…"
"Why do you think I'm stealing them for my own evil deeds?" King K. Rool asked. "And just who do you think you are to question the Kremling King, ruler of the Kritters?"
"My name is Chrom, and I clearly didn't know you were coming my way," the blue-haired warrior answered. "I was only looking for Lucina and Robin, my daughter and partner."
"Oh, you have a precious baby you're looking for, do ya? As well as a partner?" King K. Rool asked in sarcasm as the black-red cloud from up above thundered. "Listen, buddy! I ain't lookin' for your kid an' teammate! I've already got enough problems as it is with trying to steal from the Kongs when they're not around anymore! First I had to put up with Bowser's minions, now you…"
"You see that huge ship next to the Yggdrasil?" Chrom asked, pointing to the Legacy and Rathalos. "This strange creature aboard the ship is trying to claw through and attack whoever's inside. I fear that my only daughter is trapped in there, as well as my partner. I'm asking you to team up with me, since there are bigger threats than a stubborn king stealing the same loot as you…"
"What do I know of this 'threat'?" King K. Rool scoffed. Suddenly, purple lightning zapped the two Kritters that were on King K. Rool's hovertruck, which was now burning along with the Golden Banana horde. As soon as the lightning struck, more Kritters and Klaptraps crawled from the hillside, giving off a purple glow in their eyes like the Kritters that were hit. The reptilians looked at their king next to the blue-haired warrior, though not as a ruler anymore and… more like an enemy.
"What?" King K. Rool asked. "Why are you looking at me like that?" The crocodile-like creatures walked closer, grinning evilly, followed by flying Tiki Buzzes.
"Your Majesty," Chrom objected quietly, "I don't think they're on your side anymore…" The Kremlings and Evil Tikis rushed at the two fighters – the green Kritter biting, the blue Kritter spinning, the Klaptrap clamping its jaws, and the Tiki Buzz swooping downward. The four species of monsters started charging, but Chrom unleashed his Falchion just in time. Chrom attacked the same as Roy, but he was different with his Aether recovery, and wind effects to replace the fiery attacks that Roy had, plus with a tipless sword. King K. Rool grabbed ahold of his Blunderbuss, launching a cannonball and sucking few enemies in before firing them, as well as counter-attacking with his brass belly and throwing his crown like a boomerang. The objective was to get aboard the Legacy while fighting off the Kremlings that have somehow betrayed them and stop Rathalos from attacking whoever was inside.
Chrom was the first to rush, lashing at the Kritters and Klaptraps that stood in their way, slicing with powerful wind effects in a manner mainly similar to Roy, along with a moveset mixed with Marth and Ike. King K. Rool tossed Chrom onto his back as he ran, ramming into the Tiki Buzzes that landed on the ground at a bad time. Chrom then jumped off K. Rool's back, preforming a combo move with his sword that launched the Klaptraps. The Kremlings and the Evil Tikis started running after the two fighters, but they managed to get away in time across the flat landscape, killing off most of the Kremling King's minions as they rushed to the Legacy.
Once Chrom and King K. Rool got near the boarding area of the Legacy, they saw the red, dragon-like monster already broke through the hull of the ship, searching for intruders. More of the mutated Primids were surrounding the perimeter, some of them holding weapons that looked like the miniature version of the Dark Cannon. Simply rushing in without a plan, the blue-haired swordfighter teamed up with the crocodile king and started attacking few of the minor Subspace Army troops. The Primids holding the miniature Dark Cannons fired, and anyone caught in their line would be caught in an explosive blast. King K. Rool clawed his way through, throwing his crown as a projectile in the process. Meanwhile, Chrom cleared a way in by knocking out all the Primids, opening a gateway inside.
"Come on, K. Rool!" Chrom yelled, waving towards the entrance. The Kremling King was a little busy at the moment, whacking some Goombas and Koopa Troopas around with his giant fists. Eventually, King K. Rool began running towards the entrance, grabbing Chrom and busting in. After the two fighters got up, they saw the area looked empty, but just on the first floor of the ship. The two warriors looked around, seeing certain ships that were destroyed ten years ago: the Halberd, the ship that carried Donkey Kong when he was trapped in his trophy form, even Galleom and Duon being built again for real as the three-headed cyborg Jotun. As they looked around, they saw many empty display platforms with pictures of the real weapons that were there before. Devices and technology both warriors had never seen before were instead replaced by holograms as the revealed prototypes.
"What… are those things?" Chrom asked, his hand going through one holographic weapon that was a futuristic cannon on wheels.
"I have no idea," King K. Rool answered, admiring another display of a hydra-like android with what appeared to be a hundred heads, each one in a similar pose that looked like Tabuu who fired his Off-Waves ten years ago. "Even from an evil mastermind like me, this stuff is nothing you see every day…" Just then, both King K. Rool and Chrom heard yelling from someone upstairs. Looking around the room, the two fighters saw a hovering elevator with chrome plating with glowing blue outlines. Figuring this was their only way up, the duo got in, and the elevator rose up with no cables to the next floor.
The room was small, but the blue lights were bright enough to make out who was the third guest inside, whacking on the locked metal door as the only way in. The stranger whacking on the door was a black-haired mercenary, clothed blue and wielding a whip similar to Simon's. The Holy Water he grabbed out of his pocket burned in napalm flames when thrown on the ground, and his axe was leaving scratches on the steel of the locked door. The stranger turned around, noticing King K. Rool and Chrom were in the room with him.
"I don't suppose you're here for the same thing too, huh?" the stranger panted, wiping the sweat from his forehead. "I've seen the beast as well and hoping to slay it. I can still hear its roars from outside this door. It's found its prey…"
"Excuse me, but… who are you?" King K. Rool asked, Chrom approaching the stranger slowly.
"My name is Richter Belmont, the destined vampire hunter," the stranger answered, whacking the door again with his Vampire Killer. "There are fellow people trapped in here that I would like to help get out, but the door's jammed…"
"Please, let us help," Chrom said, unsheathing his sword, which glowed with blue gusts of wind. "We can help you break this door down…" Chrom then started slashing at the metal door, followed by King K. Rool and Richter slicing with their powerful weapons, eventually breaking the door down. As soon as the door broke open, the three fighters looked as they saw the creature known as Rathalos, cornering Donkey Kong, Yoshi, Kirby, Fox, Pikachu, Luigi, Ness, Captain Falcon, Jigglypuff, Peach, Bowser, Falco, Marth, Ganondorf, Roy, Mr. Game & Watch, Wario, Ike, Diddy Kong, King Dedede, Olimar, Lucario, R.O.B., Wii Fit Trainer, Robin, Duck Hunt, Ryu, and Corrin.
"Stand back…" Captain Falcon said. "I'm warning you, creature!" The monster started roaring, its high screeches so loud it stunned anyone up close, and it was just about to breath fire before something slashed at its wings. As the monster started growling in pain, the Big Blue Group and the Wolfen Assault Group turned around and saw Richter, Chrom, and King K. Rool pulling out their weapons and clenching their fists.
"Thanks for coming to help us, strangers," Marth said. "We could really use some help around here." Chrom, relieved, knelt down in front of Marth, realizing he has reunited with the Hero King.
"I've heard tales about your good deeds, Marth," Chrom sighed.
"Are you okay?" Robin asked, peeking out from behind Marth and few of the other fighters.
"Robin, am I glad to see you!" Chrom said, hugging the white-haired tactician. "Have you seen Lucina yet, my friend?"
"Actually…" Robin tried answering before Corrin tapped his shoulder. Chrom broke the hug to see what was going on.
"I hate to be the breaker of bad news to you, but…" Corrin said, pointing at Rathalos, who was crawling towards the fighters. With a mighty roar, the two groups with their new companions started getting prepared to face a powerful foe.
Rathalos first came down with a mighty swoop, expanding his claws to grab whoever was on the ground. Fox and Falco started firing with their blasters, jabbing and reflecting the powerful fireballs in the meantime. Donkey Kong, Diddy Kong, and King K. Rool jumped on top of the beast, clawing and punching through its dragon-tough skin. While Rathalos was trying to shake the three animal fighters off, Ike ran in, lashing his Ragnell with an erupting pillar of fire.
Roy joined in, teaming up with Chrom, Robin, Marth, and Corrin, the four of them avoiding the dragon flying in, catching the three animal fighters as they fell, and lashing at Rathalos' wings with their swords. King Dedede and Kirby watched out for Rathalos flying in with a powerful, fiery blast, and the two Popstarian warriors immediately started jabbing at the beast.
The dragon was showing signs of fatigue, trying to shake off Olimar's Pikmin that were thrown onto its body. As it roared again, Yoshi, Lucario, and Pikachu launched powerful projectiles into its mouth, exploding the beast from inside. However, it was just about to fire another flaming ball as it flew into the air, but Richter threw Jigglypuff in ball form at Rathalos' mouth as the rest of the gang kept attacking. Jigglypuff's light body then forced the beast to choke, weakening Rathalos. The moment the dragon coughed Jigglypuff out, having the Pokémon get caught by Peach, Luigi ran underneath its belly, trying not to be afraid as he jumped up, landing a critical punch that knocked Rathalos out.
The beast, now defeated, retreated from the hole of the ship it ripped through, flying out into the black-red darkness. The group looked at each other, wondering what's going on.
"Thought you might have needed extra hands," Chrom panted, putting his Falchion away.
"Don't mention it," Ryu replied. "By the way, what happened to the monsters that were believed to have been inside?"
"Maybe they all left for the Yggdrasil?" Fox McCloud answered in question. "Besides, I think they thought Rathalos could take care of them, and so left off for the World Tree to do… something that we can't figure out yet…"
"We saw weapons on the first floor," Chrom replied. "Well, holograms of it anyway… It looked like they were taken into the building, being shipped to this Subspace Army in a world not of ours…"
"That's why there weren't many enemies at the gate," King K. Rool snarled.
"Whatever they want inside, it can't be good," Wii Fit Trainer said.
"We're going to break in and destroy that building before any of the weapons leave," Ganondorf answered, clenching his fists.
"Just a heads-up: where's Pit?" Ike asked, looking around. "I tried asking you for the past few minutes, but it looks like the fight was too intense to even do a head count."
"Last thing I remember, Pit was about to join us," Ness responded. "Wonder where he's at…?"
"We'll know once we head into the Yggdrasil," Lucario answered. "Let's go, everyone." The warriors ran off, leaving the empty ship to one of the many gateways in the World Tree.
Inside the glass room, Shadow Mewtwo was still struggling as he was held down by Samus and Zero Suit Samus. The Shadow Synergy Stone was beginning to show signs of cracking, the Shadow Bugs that possessed his body starting to hold on as the Pokémon's skin was showing underneath. As the Shadow Bugs started swirling around his body, both Zero Suit Samus and Samus had to let go. Grabbing ahold of the small device they believed would save Shadow Mewtwo, Pichu carried it to Zelda. The princess then snatched it, ready to ask who would risk their lives. The alarm kept going, and more of the Fighting Mii Team troops dropped from the ceiling.
"This is ridiculous!" Dr. Mario exclaimed, trying to warn the Miis to back off. "Who's going to save the Pokémon while we fight the Miis!?"
"Give me the device, Hylian princess," Bayonetta answered, grabbing Snake's wrist. "Army boy and I are going to take a little detour to the dark side. You'll have to defend the Pokémon while we rescue him from within." Zelda nodded and gave the device to Cereza, who was linking it to her head.
"Be careful," Zelda said. Bayonetta then used a strand of her hair and tied her waist to Snake's utility belt, placing part of the device on the soldier's forehead. Wind was blowing hard from Shadow Mewtwo, who was still fighting the Shadow Bugs. The Umbran Witch's hair kept the two fighters close together as the wind got stronger, and Bayonetta managed to stick the last portion of the device on the Pokémon's head. Snake and Bayonetta hugged each other as the two of them turned the headset machine on, zapping them with lightning. After a sudden flash, Snake, Bayonetta, and Shadow Mewtwo were gone, leaving Mario, Dr. Mario, Samus, Zero Suit Samus, Young Link, Toon Link, Zelda, Sheik, Villager, Pichu, Ice Climbers, Wolf, Pokémon Trainer (Charizard, Ivysaur, and Squirtle), Ridley, Lucas, Little Mac, Shulk, Palutena, Dark Pit, Rosalina & Luma, and Greninja alone to face the Fighting Mii Team.
Bayonetta slowly got up, pulling her black hair back into her clothes. She looked to her right and saw Snake crawling to the Umbran Witch.
"Looks like somebody woke from his nap," Bayonetta said, helping Snake get up.
"Where are we?" Snake groaned. The two fighters looked around, noticing they were in some sort of dimension. The ground was made out of the same material as found in the Dark Synergy Stone, and the sky was pitch-black while stardust danced in the air. Darkened opal pillars formed out of the ground and Primids, as they had appeared ten years ago, emerged, staring at the warriors.
"Looks like we'll have to follow the black brick road to the land of the tortured Pokémon," Cereza chuckled. Snake and Bayonetta then pulled out their guns, ready to attack some Shadow Bugs and save Shadow Mewtwo. The Umbran Witch rushed forward along the pathway, transforming into her Panther Within and mauling the first Primids who crossed her path. Snake ran behind her, throwing grenades and firing rocket missiles, grabbing a Boom Primid from behind and breaking its neck. Bayonetta jumped on top of Snake's shoulders, light as a feather.
"Spin me right round, baby," Bayonetta said to Snake, her words as smooth as honey. Snake pulled out his pistol and shot the incoming Scope and Sword Primids while Bayonetta used her "Love is Blue" guns and fired in all directions with magical bullets from both her hands and feet. Cereza then jumped off the soldier mercenary, sweeping him off his feet and running as fast as she could while strands of her hair opened portals to Inferno, unleashing Madonna Butterfly's limbs that dealt powerful blows to the neverending Primids.
Just as soon as Snake and Bayonetta were in the clear, they saw they were in some sort of coliseum, where there was a yellow barrier surrounding them. In the center, hovering in midair, Shadow Mewtwo was about to give up. The Pokémon had been through a lifetime of struggling, and the Shadow Synergy Stone finally broke, its shards flying all over the place. Once the Shadow Bugs were free, they took on the form of their possessor, forming into a real "Shadow Mewtwo", which looked the same as before, but with the Shadow Synergy Stone gone, the Pokémon's body the same color as the Shadow Bugs, and his eyes glowing an eerie yellow. The new and improved Shadow Mewtwo touched down on the ground, his feet barely touching, glaring at Snake and Bayonetta.
The Shadow Bug fighter flew into Solid Snake, slamming him into the yellow barrier surrounding the coliseum. As Shadow Mewtwo was about to strangle Snake, Bayonetta grabbed the Shadow Bug warrior with Umbra Witch magic, smacking him and tossing the possessed creature into midair before she flew up with an uppercut. However, Shadow Mewtwo grabbed her by the neck, tossing her down and unleashing a rain of Shadow Balls upon her.
Snake flew in holding onto a drone, hopping on top of the possessed Pokémon's shoulders. Snake managed to get Shadow Mewtwo down on the ground with a series of C4's planted on the Shadow Bug fighter's chest. Snake loaded a rocket missile, and Bayonetta ran to his side to fire magical bullets, aware that Shadow Mewtwo might reflect them with Confusion.
The two fired their weapons, and Bayonetta transformed into her Panther Within to run faster than the projectiles. Shadow Mewtwo was about to reflect them, but Cereza transformed back to normal and placed the Shadow Bug fighter in a headlock as the projectiles hit his chest, and Snake came in for the final blow with a fist punch.
After Shadow Mewtwo was defeated, all the Shadow Bugs vanished in midair, and the only thing that remained was the trophy that they had possessed. Bayonetta slowly walked towards the prize with Snake next to her, wondering how to get their enemy back.
"How do you think you save another fighter?" Bayonetta asked, playing with her white gloves. "Do you cast some sort of spell, or…?"
"Actually…" Snake answered, kneeling down next to the trophy. With a single touch of the golden base, Snake gave life back to the trophy, and it started glowing with rainbow-like sparks. Once the fight was over, Mewtwo was awakened, with pale white-pink skin and a darkened magenta tail, not with a black body and an orange tail. The Shadow Synergy Stone fused to his left shoulder was gone, and he saw the two fighters who saved him.
"What… what happened?" Mewtwo telepathized.
"You were imprisoned by the Subspace Army," Snake answered, "but we brought you back."
"Thank you," Mewtwo telepathized. The legendary Pokémon slowly levitated off the ground, sighing in relief that the nightmare he had suffered through was over. Suddenly, the yellow barrier broke, and the world that Mewtwo was trapped in was dissolving, along with all the Primids that made this place their home. Bayonetta dragged Snake and helped him stay close to Mewtwo as she wrapped more of her hair around the three of them, hoping they would stay together.
"Now that we're done, do you think you could warp us out of here?" Bayonetta asked Mewtwo.
"It has been a long time, but I'll try," Mewtwo telepathized in answer. Using his powers, the Pokémon warped both himself and the two fighters out of his world before it closed in, revealing only darkness. The moment the three warriors came back to the glass room they were stuck in, they saw many of the fighters they were stuck with from the beginning already attacking the Fighting Mii Team.
"Did we miss anything?" Bayonetta asked.
"You missed plenty," Zero Suit Samus answered, blocking an attack with her Plasma Whip. "Basically, while you two were gone rescuing Shadow Mewtwo, an enemy Shulk calls Metalface arrived in the scene, blasting lasers and clawing his way through everyone, hoping to destroy us all…" When Mewtwo, Bayonetta, and Snake looked, they saw a huge, spiky robot which was presumed to be Metalface, Shulk's rival. The Mechon grabbed ahold of Shulk, who was trying to pull out his Monado Arts.
"Well, well, well," Metalface laughed. "If it isn't Monado Boy, trembling in my clutches. Did your fairy godmother die again in your lucky winning streak?" A sudden burst of energy then flowed from Mewtwo, who blasted the entire glass room, bursting the windows and sending the Fighting Mii Team flying. The legendary Pokémon looked at the Mechon, generating purple sparks from his hands. The other fighters joined up to his side, and Shulk squirmed enough to grab ahold of his weapon, slicing Metalface's hand off and dropping onto the ground.
"You'll pay for this, traitor," Metalface groaned, pointing at Mewtwo. "Yes, you'll pay…" Samus and Shulk ran up to the Mechon, avoiding its laser beams. The bounty hunter then jumped, releasing bombs from her Power Suit, while the Bionis pulled out his blade and started glowing purple, the both of them attacking Metalface. Dr. Mario twirled around in his cyclone move, followed by both Young Link and Toon Link, who latched onto Metalface's jetpacks and clawed their way through with their swords in their left hands. Mewtwo floated in with a quick purple slice from his hands, and Greninja used water from its long tongue to create a shuriken powerful enough to slice through Metalface's body.
Snake and Bayonetta tried staying out of this as best as they could, helping out with only their projectiles, since they were already in a boss fight. Zero Suit Samus, Palutena, and Rosalina with her yellow Luma avoided the Mechon's claw attacks, the three women kicking and jabbing. The Ice Climbers, Wolf, Pichu, and Red's three Pokémon went in, weakening Metalface even more, followed by Villager who landed a big hit with his shovel and a KO Punch from Little Mac. As soon as Metalface was defeated, he went out in a massive explosion, the remains of his robotic body flying off into the depths of the Yggdrasil, crying, "Not fair! I cannot lose!" The warriors looked at the hole the Mechon ripped through, which made a doorway and a shortcut deeper into the building.
"Looks like we have a way in," Rosalina said, the Luma of hers hugging close.
"What about Cloud and Link?" Mario asked in objection. "Aren't we supposed to wait here until they come back with Dark Samus?"
"I'm afraid in times like these, they're forced to find us again in some way," Palutena answered in grief, floating with Mewtwo to the ripped hole in the wall.
"I know a way where we can destroy the weapons before they leave the building," Mewtwo said. "The only thing to do is self-destruct the Yggdrasil at the control room in the top." All the fighters in the group nodded, walking off to the top of the building leaving a destroyed room behind.
