You may have noticed that the game mode called The Subspace Emissary does not feature any dialogue. It’s still fun that way, but there may have been some story-related items that didn’t fully make sense.
So let me tell you some of the story background you couldn’t have gleaned from the movies. There are some big spoilers here, including the final boss, so you may want to skip this post if you haven’t beaten it yet!
<Tabuu and the Subspace Army>
First, Tabuu, the embodiment of Subspace appears. He wants to cut the world our main characters live in to pieces and drag it into his world. He hides himself in Subspace, watching our world vigilantly.
Tabuu himself cannot leave Subspace. That’s why he has to prepare an army and a leader for the offensive into the other world.
<Master Hand and the Chains of Light>
Master Hand is the master of our world. Tabuu studied Master Hand and the fighters, and this knowledge leads him to use Master Hand for his plans here.
Chains of light bend Master Hand to the will of Tabuu, who uses Master Hand to enlist the likes of Ganondorf, Bowser, and Wario. He gives each of these minions a Dark Cannon and tells them to hunt down any talented fighters that might stand in the way of the Subspace Army.
Master Hand is now more a part of the Subspace world than he is a part of our own.
<What Binds Ganondorf, Bowser, and Wario>
Ganondorf pretended to swear allegiance to Master Hand, all the while planning to usurp power from within. Bowser is relatively loyal to Master Hand, but he does not care for Ganondorf. Wario cares very little for the actual objective he was given and wants to continue just doing whatever he likes.
And of course, none of them know about Tabuu.
<The Ancient Minister>
And how will this world be cut into pieces and dragged into Subspace?
Tabuu has had his eye on the advanced technology developed on the Isle of Ancients. This mysterious island hangs suspended in the sky and gives home to a group of robots. No one knows how long they have been there, but they have existed for ages without interfering with other civilizations.
Life on the Isle of Ancients revolved around a single leader, the Master Robot (also the Ancient Minister, as we later learn). The other robots gave their unwavering loyalty to the Master Robot and existed in peace.
But now Tabuu has taken the entire island hostage. The Master Robot wants to avoid losing so many of his brethren to Tabuu, so he reluctantly agrees to be the main front of the Subspace offensive, and begins development work on the Subspace Bombs.
The Master Robot decides to disguise himself as the Ancient Minister out of shame for his own decision to work with the Subspace Army. The Dark Cannons are also being developed and built on the Isle of Ancients.
<Mr. Game & Watch>
Tabuu takes notice of the peculiar qualities of Mr. Game & Watch’s body mass. He uses these particularities to create a nearly infinite number of shadow bugs, which he then uses to create the Subspace Army.
However, since Mr. Game & Watch does not have any concept of good and evil, he is unaware of the effects caused when he is used in this way.
<The Battleship Halberd>
Tabuu also has his eye on Meta Knight’s ship, the Halberd, as a means of transportation for the Subspace Army.
Using the Subspace Army, he launches a violent attack on Meta Knight and takes the ship for his own. During the attack, King Dedede engages Meta Knight, unknowingly making it impossible for Meta Knight to repel the Subspace Army’s attack.
The circular shockwaves emitted when Tabuu spreads his wings are called Off Waves. This devious technique is capable of immediately transforming many fighters in distant locations into trophies. You could say that this power alone makes Tabuu a nearly invincible opponent.
After Sonic breaks one of his wings, the Off Waves he emits become weaker, but they still have enough power to instantly KO a fighter. You must avoid them at all cost when fighting him.
<King Dedede’s Actions>
King Dedede learns of Tabuu’s true nature and the power of his Off Waves during the taking of the Halberd. He begins to worry what will happen once all of the fighters are turned into trophies. Once that happens, there will be no one left to restore the frozen heroes, and the world as we know it will end by Tabuu’s hand.
So he develops a special brooch. The brooches are set to work on a timer; when the timer runs down, the brooch will restore a fighter from his or her trophy form back to the original form. All you need to do is set the brooch on a hero that had been turned into a trophy and leave it there.
When King Dedede learns that Bowser and Wario have joined the Subspace Army and are turning fighters into a collection of trophies, he decides to start his own collection. He hides the fighter trophies he collects in his castle, thinking the brooches will bring them back eventually if something goes wrong, but...
He ends up using the brooch he had made for himself on Peach (or Zelda), and intends to make another one for himself later.
<The Self-Destruction of the Isle of Ancients>
Ganondorf takes control of the robots and forces them to blow up the Isle of the Ancients so that he can tear a hole in space large enough to fit a Subspace gunship through.
Once the mass production of Subspace gunships yielded a certain number of units, it would then be possible to launch all of them through the hole at once. Once the gunships were in our world, there would be no way to stop them from dragging all the remaining pieces of our world into theirs. Once that happened, there would be no more need for the Isle of Ancients or the Subspace Bombs.
<The Subspace Gunship>
The basic plans for the gunship were based on technology from the Isle of Ancients, but construction was handled by the Subspace Army inside Subspace.
The gunship was meant to be Tabuu’s trump card, but the valiant attack by the heroes neutralizes the threat.
<The Great Maze>
Tabuu has begun to reconstruct some of the pieces he tore out of our world into a nightmarish maze. The maze extends even farther than you realize.
The shadowy versions of fighters and the reincarnated bosses from earlier encounters were created based on detailed analysis carried out by the Subspace Army. They were placed here to guard the labyrinth.
<What Happened to the Isle of Ancients?>
In the ending (or new beginning) of the game, the spot marked by the shining "X" is where the Isle of Ancients was. When Tabuu and the Great Maze were destroyed, most parts of our world returned to normal, but the effect of so many Subspace Bombs going off at once made it impossible for the Isle of Ancients to return to normal.
The taking of the battleship Halberd, as well as the scuffle between King Dedede and Meta Knight, were not shown in the game, because those scenes unfortunately had to be cut.
So that’s the inside scoop for you.
Hopefully, this post was able to shed a little light as to the motivations of the characters in the story.