The trio of Marth, Meta Knight and Ike continued quickly through the wasteland, cutting down another swarm of Subspace foes in their pursuit of the Ancient Minister. Tragically, they soon come to a cliff edge and can only watch as the Ancient Minister flies off, a bit shaken from Ike's earlier blow, but unharmed.
Out in a field, a Waddle Dee walked along harmlessly before running into Luigi, who had recovered from his earlier panic about the Stadium blowing up. Preparing to regain his courage and face this new enemy, Luigi stood as bravely as he could before the Waddle Dee...who walked by harmlessly. Luigi let out a light sigh of relief before seeing another Waddle Dee had walked up to him. He leaped back and resumed his fighting stance, only to be struck from behind and transformed into a trophy. However, this was from a stand of some kind, tossed by none other than King Dedede.
"Perfect!" exclaimed King Dedede. "I'd have preferred Mario, but he should do fine."
"Your highness, our recon has spotted Wario heading this way with more trophies," reported a Waddle Dee.
"Ah, even better," said the king. "Hide and wait for the chance to attack."
King Dedede and his troops ducked into hiding as Wario approached. He drove a small cart of some kind of a grappling arm for easy trophy acquisition. In the bed sat the trophies of Zelda and Ness. As Wario drove, he spotted the Luigi trophy left out on the road. Unable to resist, he pulled over and got out to take a look.
"Huh, I wonder who-a did this," Wario mused briefly. "Ah, who cares! One more for me! Wa-ha-ha!"
As Wario gloated, the Waddle Dee army charged from the trees and had him surrounded. In the ensuing ruckus, the Luigi trophy flew from Wario's grip and landed in the cart. Grinning with success, King Dedede drove off, his army making haste to keep up with him. Wario soon recovered and realized what had happened.
"Hey, come back-a here with my stolen statues!" he cried.
Deep in the forest, not too hard from the Stadium's location, Link and Yoshi continued their search for the missing Toon Link.
"Nothing so far," grumbled Link. "Where could he have gotten to?"
"Huh? What's that up there?" asked Yoshi.
Just above, the Halbred swooped low over the forest. As it did, more blobs of darkness fell to the forest floor and a wave of Prismids and puppet-like enemies called Puppits began to form in front of the two.
"What the heck are these?" asked Yoshi.
"I don't know, but they sure don't look friendly," said Link. "Let's take 'em out!"
The two deftly made their way through the hoard of enemies. Along the way, they continued to pursue the Halbred in hopes of catching up to it and finding out why it was dropping enemies so. Unfortunately, like Meta Knight and his group before them, an inconveniently placed cliff kept them from pursuing it directly for the time being.
"I guess we'll have to go around," said Yoshi.
"If only I had Epona!" grumbled Link. "Say, Yoshi-..."
"Don't even think about it," said Yoshi.
In the Halbred's storage room, safely behind beneath a cardboard box, a secure transmission was sent out.
"Slippy, come in. Do you read me?"
"I hear you. Have you discovered anything?" replied Slippy.
"It looks like these Dark Cannon weapons the Subspace Emissary has been using performs some kind of transformation process on its victims, turning them into giant trophies. From the specs I've gathered, it doesn't seem like the victim is able to move or is even aware of their surroundings. I'm sending you the specs now."
"Receiving...all right, we've got it. We'll start on developing a counter-measure right away."
"I'll contact you again when I have more info. Snake out."
It had taken much effort to get as far as she had undetected, but Samus had finally succeeded in making her into the Research Facility of the floating island. Dropping down through the air vent, she landed safely and began her mission. Nothing would stop her from recovering her Power Suit. But as she took the R.O.B. sentries that stood in her path, nothing was prepared for what she saw as she progressed deeper and opened a door into one of the reserve rooms.
"Pikachu?" she gasped in surprise.
Pikachu had been trapped in a glass tube, connected to what appeared to be a large battery. Every few seconds, the machine would drain a burst of electricity from Pikachu, causing noticeable pain to him in the process. Samus quickly flipped her Paralzyer into its Plasma Whip form and shattered the tube with a deft strike. That sounded the alarm and a horde of R.O.B.s entered to attack, but with Pikachu free and able to help her, Samus was able to bash her way through.
As the duo progressed their way deeper into the heart of the base, they soon came found themselves in one of the control rooms. A bevy of viewscreens showed off various locations both within and outside of the base. It was one of those screens that Samus found the location of her goal.
"There you are," she said to herself.
"Pika?" inquired Pikachu.
On the location of one screen was Samus' Power Suit, situated deeper inside of the base. With their new destination determined, the two began to trek even deeper into the base.
Meanwhile, the SPs had reached the Palace of Power, which had be heavily damaged in what was no doubt a difficult fight.
"Hurry!" exclaimed Metal, pulling furiously at the door to get in.
Saiyaman walked up to the door and pushed it open.
"...right, I knew that," said Metal calmly.
Once inside, the SPs were instantly confronted by Mother Brain. However, Mother Brain had transformed herself into her walking abomination form from Super Metroid, a brain onto top of a cybernetic body. Even more horrifying were the trophified forms of Captain N, Princess Lana, Simon Belmont and a fourth figure.
"Oh no, we're too late!" gasped Digi.
"It's even worse!" cried GG. "That's Professor Hector, creator of the R.O.B.s!"
"Correct!" cackled Mother Brain. "With him under my control, it's made it all the easier for the one who plans to carve up the world to fulfill his plans! And before you ask, no, I'm not telling you who that is! Prepare to die!"
In a split-second, Mother Brain fired a devestating laser beam from her hands, forcing the SPs to dive to safety. In the confusion, the Geno doll GG had been carrying fell to the floor. As the SPs picked themselves up to fight, the doll suddenly was surrounded in a flash of light as Geno inhabited it once again.
"Ha, I'm back!" he exclaimed. "I've come to help!"
"That's great!" cheered Saiyaman. "All five of us can take her!"
"Maybe so, but that's why I prepared this!" cackled Mother Brain.
Before anyone knew what was happening, a flurry of Dark Cannon rays burst forth from the floor. Both the SPs and Geno were quickly turned into harmless trophies and left to fall to the floor.
"Wa-ha-ha! I did it! I succeeded where all the other Stadium villains failed and I finally beat the N-Team to boot!" cheered Mother Brain.
As Mother Brain savored her victory, the spirit of Geno slipped out of his trophy body and floated to safety, hovering near the Palace of Power for a bit.
"Crap, that went bad," he said to himself. "I'll need help - and maybe a new body too - to get them back."
With that, Geno took off, looking for other Stadium members to help him.
As Peach and Kirby continued along their way, Kirby caught what he thought was King Dedede out of the corner of his eye.
"Hmm? What was that?" he pondered.
Kirby soon dashed off to confirm what he saw.
"Hey, wait a minute!" called Peach.
Peach turned around to see who it was, but it was too late. In an instant, the Dark Cannon had turned Peach into a motionless trophy on the ground. Bowser grinned a demented grin while his Shadow Bug duplicate dissolved and enveloped the Peach trophy.
As Mario and Pit tirelessly continued their journey to find the Ancient Minister, a dark doppelganger of Peach, formed from the Shadow Bugs, took aim at them with a Dark Cannon. Before she could fire, a slice from the Master Sword cut the device in two, causing it to explode. Dark Peach turned to find Link standing by, while Yoshi caught up to him.
"Whoa, what happened to Peach?" asked Yoshi.
"I don't think that's Peach," replied Link. "She just tried to take out Mario."
Dark Peach glared at them and the battle began. She started off with a quick Vegetable toss, but Yoshi's fast tongue caught it, leaving her up open to a bomb in the face from Link. While she was stunned, Link pressed the advantage and began to slice into her. Dark Peach eventually managed to roll behind Link and attack, but Yoshi got her with a Ground Pound.
The two-on-one advantage proved to be the key aspect to victory for the duo. Dark Peach was only able to focus on one of them at a time, so as the battle continued, the two wore her down. Finally, Link delivered a mighty blow with his Spin Attack, slicing Dark Peach apart and causing her to dissolve into Shadow Bugs.
The sounds of the battle caught Mario's eye and he looked over just in time to see the Dark Peach dissolve into nothingness. At the sight of see who he thought was Peach die, Mario went into a fury unlike any he'd been in before. He went ran in a mad dash towards Link, who heard the sound of him coming and was just barely able to dodge before Mario could land on him with an powerful punch.
"Mario? What's the big idea?" asked Link. "Wait a minute...where's Zelda? Wasn't she back at the Stadium with the others?"
"That doesn't-a matter!" exclaimed Mario. "You killed the woman I love and you will-a pay!"
"What? That wasn't...wait, are you saying you let something happen to Zelda? Curse you, Mario! I won't let you walk away from this!"
"Whoa, guys! Isn't this going a bit far?" asked Pit. "Let's stop and talk about this for a second."
"Mario, hold on a bit!" exclaimed Yoshi. "We can explain!"
But it was too late. Both of them, too lost in their sorrow, dove into battle against each other.