Well, the fact that this update is for a story mode is pretty obvious, and the fact that "???" has it's own subsection means that more on the story mode will soon follow, but for now I think all we can do regarding this update is wait for new details on it. Until then, there is really nothing we can grab from it, so I think it's a little pointless to guess. The only thing we can surely know about it is that these story mode updates will be extremely rare. The fact that the backround on this update was black means not that the story will be particularly dark, but that the update is extremely important. Important enough to warrant rare updates....but...
My thoughts on the story mode are this: I think mostly everybody has gotten it right so far. Mario and Kirby broke the rules of the Smash World, and thus they need to be punished. However, not by Metaknight or Bowser like people seem to think. This makes no sense, seeing as both Metaknight and Bowser are trophies, just like Mario and Kirby, so why would they be serving Master Hand? The thing coming to punish Mario and Kirby are those robot, purply things (which I will call "Puppets" from now on). These Puppets are the slave type things of Master Hand, whose purpose is only to punish those who broke the rules. If you disagree with me on this, look at the Puppet's eyes. They show absolutely no emotion, and look as if the Puppet was programmed only to serve, which is exactly what I think. Also, the boxing gloves furthur this theory, as they show the ability to fight. The Puppets didn't show up in previous Smash Bros. games simply because nobody broke the rules. In SSBB though, the characters (at least Mario and Kirby) got sick of all of that, and thus created a storyline that was supposed to be in SSBM, but was scrapped due to time restraints. The push backs in the release date were announced to the devs could create and flesh out this storyline, otherwise I think Sakurai has finished the game.
The real question that comes into play here, is why does Metaknight show up? Metaknight's purpose could drastically change my theory, which is why I think we can only wait for more details at this point...