Basically, the plot was that Smash 64 was a collection of the universe's best fighters. Each one was (no pun intended) hand-picked by Master Hand and Crazy Hand. However, the four cut characters (Bowser, Mewtwo, King Dedede and Pit) were also included. Master Hand's side was made up of Mario, Link, Kirby, Pikachu, Ness, Jigglypuff, Luigi and Pit, who were as good as can be in a story like this. The Crazy Hand picked guys were Bowser, Dedede, Mewtwo, Donkey Kong, Yoshi, Captain Falcon, Fox, and Samus. They were kind of the bad guys, but here's where it gets real:
There were no real good or bad guys. Bowser was a misunderstood fellow, Mewtwo was silent and powerful, therefore considered evil, and Dedede was just a douche. Crazy Hand manipulated those three especially into playing evil roles, but the other five on that side were just possessed. The "villains" were imprisoned, and all was good after Crazy Hand was defeated by Master's team.
Then, onto Melee.
Everyone from that game appeared except Young Link, Dr. Mario, and Pichu, and added in their place were Wario, Ridley, Samurai Goroh and Wolf. Along with Ganondorf, these five were legit evil, and even broke the original three villains out of jail. Also, as a side note, characters aged since their introduction in the original. So, everyone from Melee got two years older, whith Falcon being the oldest, and Samus, Mario and Bowser being not far behind. The youngest were Ness, Kirby and Pit in that order. The villains fought the heroes, and lost and once again imprisoned.
Brawl added everyone but Toon Link, who was replaced with Skull Kid. Brawl was pretty much SSE with dialogue, and the fact that the villains were broken out once more, this time completely destroying the prison. I'm writing Smash 4 currently, and I think it's more interesting than any of the others at this point.