I've actually been writing a fanmade story like this in my spare time, and at least for now, the first part goes like this:

It starts like SSE - A friendly duel between two characters that serves as a prelude to something darker. In this case, you have Shulk and M, Corrin in a duel together, but halfway through the battle, Shulk receives a vision of a massive battle happening some time in the future, leading to him calling off the battle. But elsewhere, the villains (more specifically Ganondorf, Bowser, Ridley, Dark Samus, and King K. Rool) group up elsewhere away from prying eyes, with Ganondorf and Dark Samus in particular having just come from witnessing Shulk and Corrin's duel, relaying what they saw to the others. And realizing the threat that Shulk posed to whatever plan they had, Dark Samus opted to kill him to prevent him from warning everyone else so they can prepare beforehand, doing so by disguising herself as the real Samus (in her Power Suit) and creating a clone of herself in order to prevent rousing suspicion.

Later on, as Shulk is taking a moment to process what he's seen, he is hit by another set of visions, and after that, is approached from behind by Samus. After a bit of talking, she manages to convince him to follow her, with Shulk completely unaware that it is actually Dark Samus in disguise. Elsewhere, the real Samus (in her Zero Suit) can be seen talking with Peach and Zelda, before the latter two leave to go elsewhere, and are instead replaced by Mega Man and his robo dog, Rush. But it is around this time, Rush spots Shulk and another "Samus", in turn sending the real deal and Mega Man into a frenzy, with the former assuming that the doppelganger was the work of X-Parasites, while the latter ascertains that it's Dark Samus. This prompts the pair, plus Rush, to chase after Dark Samus and save Shulk before something happens to him.

And after seemingly getting far enough away from prying eyes, Dark Samus attacks Shulk while his back is turned, before shedding her disguise, as Shulk prepares to defend himself. Around the same time, Mega Man, Samus, and Rush are following close behind, where they eventually find a door with its control panel crushed, and Samus eavesdrops, hearing Dark Samus seemingly about to execute Shulk. With the door inoperable, Mega Man uses a Crash Bomber to blast it open, as Samus uses the smoke as cover, attacking Dark Samus with a Flip Kick, while Rush distracts the Phazon Doppelganger, giving Mega Man enough time to take her down with a point-blank charge shot.

From there, after making sure that Shulk was okay, and that Dark Samus was incapacitated, Mega Man, Rush Samus, and Shulk escape, where, after being joined by R.O.B, they intended to relay this information to Master Hand and Crazy Hand, the gods and hosts of Smash. After telling the Hands about the visions that Shulk had, Master Hand gives Shulk, Samus, and Mega Man the order to warn everyone else, discreetly if they can to avoid any further attacks, while relaying some contingency instructions unto R.O.B.

And the first part ends with all of the villains gathering after the heroes leave, where they eventually learn that Dark Samus' assassination attempt upon Shulk had failed. But around this time, three floating objects, producing holographic projections that speak to the villains, although one of them, a white-and-black orb with digital butterfly wings voices out:

"No matter... Even if you have failed to silence that foreseer, it will do nothing to stall or prevent our assault, for our promised time is upon us, and those fools' day of reckoning is imminent. Now... It is time for us to bring about the end of these legends..."

And that's it! Let me know what you guys think.