This post is really, really late, seeing as how Super Smash Bros. Brawl has been out for a long time now, but I was thinking about the story mode recently and my theories on it back when the game first came out. As such, I want to record them here for all of you.
Warning, spoilers follow.
The basic plot of the “Subspace Emissary,” or the story mode in Smash Bros. Brawl, is that a mysterious being called the Ancient Minister is detonating Subspace Bombs and destroying parts of the Smash Bros. universe for some diabolical scheme. We later learn that the Ancient Minister is actually the Robot Operating Buddy that was originally released with the Nintendo Entertainment System, and that R.O.B. is being controlled by Master Hand, a gigantic disembodied right hand that is like a “god” of sorts. However, it also turns out that Master Hand is being controlled by a being who rules Subspace named Tabuu, who is also the ultimate opponent in Subspace Emissary.
Looking back at the original Super Smash Bros. for the Nintendo 64, the game’s cinematic opening implies to us the true identity of Master Hand (and by extension the left “Crazy Hand” from Melee on). Master Hand’s domain is a room which contains a desk, a chair, and a toy chest from which he pulls out dolls of his favorite Nintendo characters. In other words, Master Hand is a kid who is just having fun with his toys and his video games, and that is why he is the default final boss in the series.
Who is Tabuu, then? Well, he is a being more powerful than Master Hand, who controls and restrains Master Hand against the hand’s will. He is capable of attacking with “Off Waves,” which renders the Nintendo (and Sega and Konami) heroes lifeless. He is described in the game as “having been born in a vastly foreign realm” and also “possess[ing] great leadership powers.” If you look more closely, you will see that the true identity of Tabuu is Master Hand’s father, or specifically the father of the kid playing with his video game toys. He rules subspace as a great leader and he is capable of turning “off” the child’s games.
The greatest evidence towards Tabuu being a child’s imaginary representation of his dad comes in the form of R.O.B. Prior to the start of the Subspace Emissary, Tabuu attacks R.O.B. and forces it and its loyal followers to do his bidding or risk further destruction. Why is R.O.B. of all characters the titular subspace emissary? Why is he the border between the Smash world and Subspace? If you look at what R.O.B. actually is, then the answer becomes clear.
R.O.B. was originally released as a toy to go along with the NES to play R.O.B.-specific games, and was instrumental in tricking convincing parents to buy a video game entertainment system for their kids. R.O.B., to those parents and even some kids, was the most visible part of the NES. More importantly, R.O.B. in his original games exists as both a character on-screen and as a physical object in the real world, making R.O.B.s the ideal messengers between Subspace (the real world) and the Smash world (video games and imagination).
So in actuality, the “Subspace Emissary” is an allegory for a father telling his child to stop playing with toys because they have to go do something away from the realm of video games and fun, like go visit grandma. The child, i.e. “Master Hand,” is thus captured by the evil “Tabuu,” who seeks to turn everything “off” and control everything. The father destroys and enslaves the R.O.B.s first because they are the easiest targets and the only ones to truly be both physical and imaginary. The child/Master Hand in turn must be saved by his own creations, the characters of Smash Bros. Whether the “defeat” of “Tabuu” happened in reality or purely in the mind of the child is sadly unknown.