Synopsis
All of them - all the characters of this great series didn't see it coming: a machine created by the Subspace Army to copy the abilities of them. And who had switched it on? It was none other than the two merciless evils - Ganondorf & Bowser. Now, to add onto this "machine", the Assist Trophies and Pokemon were also copied. Now, along with Ganondorf & Bowser, they must destroy that machine for the greater good.
How It Occurred
Merciless wielder of the Triforce of Power, Ganondorf, had founded the last remaining Subspace Bomb days away from the imploded Subspace Bomb Factory. He'd taken it and unluckily for him, Bowser was apparently there as well - at the same time, at the same place. Bowser stared at him, thinking about how he'd betrayed him by turning him into a trophy. Then, with great force, he'd charged Ganondorf and let him drop the last Subspace Bomb.
As the two were going head-to-head with each other, the Subspace Bomb had made strange noises due to it being activated - accidentally, by Ganondorf. The Subspace Bomb stood up by itself, and pulled the surface in the area into it. Then, with great shocks of electricity and lightning swiveling around the Subspace Bomb, it had released rushing wind. Soon, it had pulled out a controlling area.
"What is this?" Ganondorf had wondered while gazing at the machine that had unexpected abilities. "What are these controls for?"
The controlling area soon displayed every individual of the Smash series. And soon, it showed every individual of every video game, every franchise, every movie, ever made. They didn't recognize them, so they only continued with every individual of the Smash franchise.
Bowser soon had unknowingly tapped onto 'All Individuals' while jabbing Ganondorf and when he jabbed again, he unknowingly tapped onto the 'Copy' button. The machine soon went into 'crazy' mode again and released every individual of the games - including the Assist Trophies and Pokemon. Excitedly, Ganondorf and Bowser gazed at each other thinking of what an army they could build.
The Backstory of the 'Cloning Machine'
As if that wasn't enough; the backstory of the 'Cloning Machine' is quite simple [or maybe, it is.] The Subspace Army, commanded by Tabuu, had been observing the smashers for years - before they had initiated their plan. Staying hidden in the dark of rooms and continuing their scheme, it hadn't been long before it had all arrived. The implosions, one of the biggest points of some smashers' helplessness - it had all occurred, and it had all ended.
Tournaments from here and there had distracted the fellow smashers, being unknowing of what had arrived. And now, their next problem would be two merciless and ruthless evildoers and a small-but-powerful cloning machine ready to cause impersonation of smashers.
Ambush of the First Clones
The first clone had taken mere seconds to be created by the machine. It had taken an imitation upon Ganondorf, whom the original disliked [and even tried stopping.] The clone of Ganondorf had moved away from the two ruthless and merciless kings and dashed into the Temple of Hyrule. There, entering into the temple, had the clone seen the entire group of Smashers having a large tournament.
The clone had silently and noiselessly approached to the unknowing smashers and well, all the Pokemon and Assist Trophies and living items, and was about to execute the Warlock Punch with one swift stroke. Soon, being obliviously dragged away, the clone had seen a whole group of clones with him. Soon held grudges with each other and felt as though they could defeat the true smashers in the tournament and/or fight each other. But their main goal was to wipe out the whole existence of those original individuals.
Each and every clone had a different level - some were skilled than others, and it would probably become a huge downer when the true smashers would discover one bad thing - the clones can take different forms.
Then, while some were planning upon how they could fight, the rest had just rushed in to separate the smashers and defeat them - one by one. Hunt or be hunted, it would all assure one thing - it's now about survival.
CRASH! THUD! SLAM! BOOM!
So much had occurred in a small moment of time. Each and every single individual had been moved, scattered, into all sorts of different locations. That had included Ganondorf and Bowser, whose expectations didn't include betrayal of their "minions" as one of them.
Destruction of the Cloning Machine
All the characters there were had arrived at the scene of the battle, gazing at thousands of millions of clones. They had all attacked the machine at the same time - destroying it slowly. Clones and clones were approaching to attack the characters - but, due to the characters' superiority in combat and strategy, they had been out of the field of battle planning on how they could defeat the originals.
CR-CR-CRACK!
Each hit a character gave would slowly hurt the machine - and soon, it would be destroyed. Once the machine had been completely finished, it was the clones' turn to be finished.
The Ending
There were, however, too many of clones in all the locations of the universe. The original characters would, though, keep fighting until they meet the end of the clones. Continuing their normal lives of competition, and trying to find the end of clones, the characters would separate [sometimes doing tournaments, but coming to anyone's help when needed.]
It was soon time to finish off the clones - completely.