Chapter 2: An invader in Sonic's world:
With the return of Kirby and knowing he had succeeded in helping Megaman and Protoman, Future Rosalina smiled.
"Kirby, You've done a great job. Thank you." She said proudly, making Kirby smile back, before dancing a little, showing his joy.
"I cannot believe we mended the timeline with no side effects." Peach commented.
"Unfortunately it is not the end. We had another change in history. Hear us out, Mario and Luigi." Shulk said, before he told them. "You see Dr. Eggman or Robotnik, was using the Time Eater to try to erase time. All of Sonic's friends are trying to fend the off machine, but someone is slowing Sonic down, making sure he does not reach his friends."
"Someone trying to slow Sonic down?" Luigi asked, thinking it almost impossible to keep Sonic from showing off his speed. "Who?"
"That is what we are about to find out. Please help Sonic." Future Rosalina said, to which Mr. Game and Watch handed Mario and Luigi the scroll, allowing the brothers to traverse to the timeline of the blue Hedgehog.
-In Sonic Generations timeline-
Mario and Luigi reappeared in the white time space and both found the modern and classic Sonics facing off against an enemy, to their surprise it was not Dr. Eggman but the same short, balding man with a large head that had a giant 'N' upon it, only he was standing on a hoverboard and held a red ray gun.
"Sonic, are you alright?" Mario called out, grabbing the modern Sonic's attention.
"Mario? You're here too? This is a surprise." Sonic commented.
Luigi then turned to the newcomer. "Who in the Mushroom Kingdom is that? He's not supposed to be here!"
"I am Dr. Neo Cortex." Said the man. "I saw your little friend's battle against Dr. Wily there. Though I never expected the famous Mario Brothers to appear. But this is too perfect. Not only will I destroy Sonic the Hedgehog, but you two as well."
{Dr. Neo Cortex? What's the arch enemy of Crash Bandicoot doing here?} Shulk asked in surprise.
{Someone brought him here. Mario, Luigi, please stop Cortex from destroying the two Sonics!} Future Rosalina said.
"Another evil doctor trying to conquer the world? Not on my watch, Big Head!" Sonic said as he charged his Spin Dash at Cortex, who moved his board aside before he held his ray gun and fired a orange blast at Sonic, only for Mario to deflect it with his cape.
Recovering from his own attack, a frustrated look appeared on the doctor's face.
"Meddlesome heroes! Try this on for size!" Cortex yelled as he then withdrew a bomb and threw it at Luigi and Classic Sonic.
Mario and Sonic both kicked it away, just as Luigi then got a message from his earpiece.
{Can you read me? The Mii Squad should be on their way to your location. Cortex is a calculating individual. You need teamwork to bring him down!} The female voice said to them.
Cortex then turned to see a couple of Miis heading in his direction.
The first one was a male Mii, who had brown hair, black eyes and wore an orange ninja kit holding a sword.
The other is a Mii, which had short blonde spiky hair, Black Knight's Helm and Black Knight's Armour.
And finally, the other was a Mii, dressed as Fox.
"Hmph. I guess that's all for now." Cortex scoffed, before taking his leave upon his hoverboard before the Miis could catch them.
But with Cortex retreating, Mario looked at the Miis and immediately recognised the Mii in the ninja outfit.
It was Goku.
{Hurry after them!} The woman contacted them.
"Ok. We'll see you later, Mario!" Goku said as he, Cromwell and TerraFox chased him.
"So who was that guy anyway?" Sonic asked, before he then said. "Well, there's no time to worry about that now. I have to get over and save my friends!"
"That thing happens to be another scheme of both Eggmans." Mario told Sonic, making Luigi nod in agreement.
"Eggman? Figures. Anyway, I don't know how you guys got here, but thanks for the help guys. You really helped me out back there. So, care to help me a little more?" Sonic asked.
"Of course." Mario nodded.
Knowing they had his back, Sonic smiled, before he and Mario linked hands and zoomed off, with Luigi holding onto Sonic's classic self, who chased after them.
-At the final battle-
The huge Time Eater was hovering above the weakened forms of both Tails, Knuckles, Blaze and Shadow as both Eggman were in the cockpits of their mech.
However, it seemed luck was on the side of the good guys as Sonic, his classic self, Mario and Luigi appeared in haste.
"Sonic!" Tails called out in shock.
"What took you so long? You're late!" Knuckles called out.
"Sorry. Got a bit distracted by another mad doctor, but don't worry, we're not going to let Eggman win. Remember, I've beaten him every time" Sonic said.
"Wait... you're... Mario and Luigi? You're both dressed different and why are you two here?" Shadow questioned.
"We're here to help, let's just leave it at that for now." Mario said in reply.
"Ah, Sonic. I was expecting you. Soon after I take care of you, I will control the whole world!" The modern Eggman laughed madly as he was seen covered in the same evil white energy that was on Wily, something Mario and Luigi immediately noticed.
The classic Eggman scratched his head.
"Wow. Will I really get that crazy?" He asked himself.
"Sonic, I hope you brought your Chaos Emeralds. I'm sure you noticed it too. Your Eggman is being powered up by some strange energy." Mario said.
"Yeah, I noticed that too. Alright, time to scramble some Eggman, Super Sonic style!" Sonic called out as both he and his classic self powered up, using the Chaos Emeralds, both becoming Super Sonics, who then charged into battle.
"Mario, let's power up too." Luigi said as he begins to finger his pockets when...
"Not so fast!" A familiar voice to the Mario brothers called, making Mario and Luigi turn in surprise to see Wario and Waluigi behind them, only Waluigi was now wearing a Warioware outfit just like Wario's.
"Wario? Waluigi? What are you're two doing here?" Mario asked in shock.
"Wahahahaha. We knew that Samus woman would call you here. So Bowser sent us to stop you!" Wario said as he charged at Mario, to which his and Mario's fists met.
"Did you say Bowser?!" Mario questioned.
{Wario and Waluigi? They're not supposed to be here. Listen, you two have to fend them off and then help Sonic deliver the final blow on Eggman!} Future Rosalina suddenly told the duo.
"Future Rosalina... is it Bowser who is behind all of this?" Luigi asked as he ducked under Waluigi's fist.
{It looks that way, but it's not just Bowser. Just hurry and defeat them before Eggman defeats Sonic!} Future Rosalina said in reply.
Mario then snarled as he understood and threw a fireball at Wario, who dodged it, got on his bike and charged at Mario.
But acting quickly, Mario leapt out of the away.
"Hehehe. I hope you're ready!" Waluigi said as he took out a Bom-omb and whacked it with his tennis racket, causing Luigi to counter as he used his Luigi Rocket to duck away and then slammed his head into Waluigi's chest.
Mario then grabbed Wario, spun him around and threw him in the distance as Wario leapt back upwards in mid air and used his Wario Whaft move, causing a huge gassy field to cover them, which revolted the heroes until Luigi used his Polgergust 5000 to suck up the gas as he and Mario looked around to see where their rivals went.
"Where did they go?" Luigi asked.
"Blaze!" Tails called out.
Mario and Luigi turned to see Wario and Waluigi both had trophy guns and had Blaze at gunpoint.
"Surrender you two, or we'll turn this cat into our personal trophy!" Waluigi said wickedly, angering the heroes and making Mario state. "That's low even for you two!"
But suddenly, a golden flash got in front of Wario and Waluigi and Blaze was nowhere in their site, making the villainous duo look around wildly, before both glared to see modern Super Sonic had rescued Blaze, holding her close to his chest in a protective embrace.
"Still up to no good, Wario and Waluigi?" Sonic questioned, before facing Blaze and asking. "Blaze, are you alright?"
"I am alright. Thank you Sonic." Blaze replied, blushing a little from Sonic's determination to keep her protected and being so close to him.
"Damn you, Sonic!" Wario snarled.
{Wario, Waluigi, that's enough. Return to base at once.} A voice came from Wario's earpiece, which Mario heard and recognised, making him ask, stunned. "Ganondorf?"
"Changes of plans, lucky you!" Waluigi said as both withdrew a Bob-omb and threw it before them, creating a moderate sized blast, along with a cloud of smoke, which when it faded, revealed he and Wario had disappeared.
With Wario and Waluigi gone, Sonic gently put Blaze down, before commenting "First that Cortex guy and now Wario and Waluigi? Something is seriously odd here."
"You left your Classic self to stop Eggman?" Shadow then asked, making Sonic say. "I saw Blaze in peril so I had to return."
And after releasing Blaze, Sonic faced Mario and Luigi and asked. "You two coming?"
"Yeah, sorry. We're coming" Mario said as he and Luigi pulled out a feather and both becoming Cape Mario and Luigi, who flew with Sonic back into battle.
They managed to catch up with Classic Sonic and Eggman as they managed to weaken the Time Eater long enough.
"Stay out of this! This is between us and Sonic!" Modern Eggman called out to Mario and Luigi.
"Yeah, well we are cutting in!" Luigi said as he and Mario both charged up a fireball and fired them at the core of the beast.
"Curse you all! Burn! Burn to ashes!" Both Eggmans snarled as they created a huge supernova, ready to end their enemies.
{Mario! Luigi! Combine your powers with both Sonics so you can finish it!} Shulk called out.
Mario and Luigi nodded in reply, linked hands with both Sonic as they became a whirlwind of power, which struck through the supernova and came out unaffected as they shot straight through the core, making the robot scream and self-destructs and then everything turned white.
As it cleared, they found themselves back in the green fields of Green Hill Valley, where Sonic caught a chilli dog, which dropped down from the sky and he gladly took a bite.
"Still warm. Hehe. Time travel huh?" Sonic grinned as classic Sonic, Tails, Knuckles, Shadow, Blaze and the others all reappeared before them.
Sonic then turned to see Mario and Luigi about to leave as they disappeared in a flash of light as he grinned and said. "I still owe you my thanks guys. Next Olympics maybe."
-Time Nest-
Mario and Luigi returned as Peach and Rosalina smiled and greeted them.
"Great job you two. Time is back on it's source." Rosalina smiled.
"Pikachu!" Pikachu called out as he pointed out to some new arrivals.
One they recognised: Samus Aran in her usual orange top and shorts.
The others were all the Miis, which consisted of Goku, Cromwell, Bugface, TerraFox, Derukui, Steph, Catlin, Killerprod1, Kasuto, Maximus, Chandler, Steph, David and Ryoko.
"Welcome back, brave heroes." Future Rosalina said.
"Yeah, it was rough out there. I am sorry. Cortex slipped through our fingers." Samus said sadly.
"Don't worry. If they are easier to catch, we could have gotten them by now." Future Rosalina said in reply.
"Glad you all came." Samus told Mario, Link and the others, before she added. "You see... we've been using the scrolls to perform certain missions. But there has been so many changes in history that we're short handed. That is why we have to ask for your help."
"Oh, I see. So that is why you called us. But we never seen these other worlds before." Marth said.
"Well, Megaman, Sonic, Pac-Man, Cloud, Ryu, Snake and Bayonetta we already know but these new people that appearing out of their proper places of time" Roy added.
"Wario and Waluigi... I didn't expect those two to show up" Yoshi commented.
"Not to mention that Bowser is involved with this." Mario added.
Link and Zelda suddenly looked puzzled, which Peach noticed, making her ask. "What's wrong?"
"He's alive, that's impossible. I was sure I had killed him three years ago." Link said.
"I am afraid so. The one who enlists villains from different timelines and use them to sow chaos are none other than the Smash Breakers" Goku told them.
"Smash Breakers?" Diddy asked, sounding confused.
"In other words, all of the Nintendo villains." Steph told them.
"Ganondorf, Bowser, Mewtwo, Star Wolf, Meta Ridley, Wario, Waluigi, Bowser Jr, K. Rool, Marx, Porky, Metal Face, Hades... a whole bunch of Nintendo villains had learned about other worlds from the Master and Crazy Hand and now formed their own group to bring trouble." Samus explained.
"We have to find and stop them before they do anymore damage." Lucario stated.
"That is correct but we cannot leave the timelines all messed up as well. That is why we need your help" Future Rosalina said.
Mario, Link and Pikachu looked at each other in concern, knowing their villains, as always, were up to no good.
"And I am worried about Fox and Falco. We've still had no contact from them." Krystal said.
"Don't worry. I am sure they'll be fine." Shulk assured her.
-In an unknown dark timeline-
The orange creature in the purple robe sat on the ground and sighed.
"Looks like I overdid it there." He commented, while, beside him was Cortex, with his arms crossed.
"So there you two are. Cortex. Ripto." Came a voice as Bowser, the King of Koopas, appeared before them, only now he held a Gerudo mark on his chest and stomach.
"Indeed. You two are not the easiest people to find." Mewtwo commented as he floated before them and had changed his attire, to which he now wore black gloves and a red and black jacket with a Gerudo mark on the back of it.
Also appearing was Bowser Jr and the Kooplings, Wolf O'Donnel, Meta Ridley, Wario, Waluigi, K. Rool, Marx, Porky, Metal Face and Hades.
Ripto rose up in a stern tone. "Ah... Bowser..."
Then Ganondorf appeared.
He still wore his armour, but now wore a black cloak around him, which resembled his cape as he then said. "I believe I never told you both to act on your own."
"What I do is none of your business." Cortex scoffed.
But then three more figures appeared.
One is mostly a anthro fox, wearing a black and golden armor with a strap around his neck, black underwear, showing off his furry legs and he wears dark black and red armbands, and dark leggings and boots.
He also wore a dark red mask with a mark mark over his red eyes and has a Gerudo mark on it.
Another was a bird-like creature who wore a similar armour and underwear, armbands and leggings but wore a black mask, green straps and his armbands are black and blue.
And finally, was a blonde haired man with a green hat and wore a green long sleeved tunic underneath his white armour with a golden strap.
He also wore black pants, dark brown boots, gloves with dark armbands and also wore a mask, only it was different from the others, for it had a red ring around the facial area and the Gerudo symbol is in the middle.
There were something familiar about the three masked individuals, but all attention were focused on Ripto and Cortex.
"Don't order me around, Ganondorf. I don't ever recall being your servant!" Ripto snapped. "I am only cooperating with you so I can take my revenge on that dragon, but that's all."
Cortex then walked in between and said. "Now, now. We mustn't bicker among ourselves, it only makes us weaker and those heroes stronger. So you guys have what I asked for?"
"Yes and you can take it with you." Bowser Jr said in reply, withdrawing two glass beakers and gave one to Cortex and Ripto.
"The dark realm has multiplied its effect. Whoever drinks Brio's potion will gain power beyond compare." Bowser Jr said.
"Hahaha. I'll be able to crush those pesky Smash Patrol and Crash Bandicoot with a single blow. You can count on it!" Cortex cackled.
"Well then. You know what to do now?" Mewtwo asked.
"Hmph. I wonder about that." Ripto just said as he and Cortex take their leave.
"You know you could have re-programmed those two." K. Rool stated.
"They're fine" Bowser said, before stating. "Why bother anyway? Those two are wreaking havoc fine on their own."
"Exactly. Those foolish Hands told us all about those timelines and now we can exact our revenge on those enemies of ours, right, Ganondorf?" Mewtwo asked.
"Correct, Mewtwo. And besides, we have everything in hand." Ganondorf smirked as he looked at the three masked warriors who just stood silently, despite Wolf getting cross at the fox warrior.
A/N: Again accepting new Miis and worlds when requested. Next is Pac Man's world.