Super Smash Bros: The subspace Emissary

Prologue

The story begins with Tabuu, the "embodiment of Subspace". Tabuu resides within Subspace, a realm of empty darkness, and wishes to destroy the World of Trophies by breaking it into pieces and dragging them into Subspace. Tabuu himself is incapable of leaving Subspace, but he can observe the world and manipulate its inhabitants (referred to as "Smashers" from this point on), in an effort to create an army with which to carry out his plans.
Tabuu first turns his attention towards Master Hand, the master of the world. Tabuu captures Master Hand with Chains of Light and pulls him into Subspace, giving him an effective puppet to command his future army in the real world. Next, he comes upon Mr. Game & Watch, who, as a two-dimensional being in a three-dimensional world, has unusual properties that make it possible to create a limitless amount of Shadow Bugs. Tabuu captures Mr. Game & Watch in order to produce Shadow Bugs, with which he creates the Subspace Army. Mr. Game & Watch is claimed to be unaware he is being used to create the army.
With the Army formed, Tabuu turns towards the Isle of Ancients, a floating island of advanced technology. The isle is inhabited by a society of peaceful R.O.B.s led by a single Master Robot that have never before interacted with other races. Tabuu needs the island's technology to produce weapons capable of cutting the world apart, so he uses his new army to take the entire island hostage, and force research on such weapons. The Master Robot reluctantly surrenders and allows this to occur, in order to avoid the presumably threatened genocide should they refuse, though he disguises himself as the Ancient Minister out of shame for allowing it to happen.
With the Isle of Ancients under his command, Tabuu attacks the Halberd, seeking a transport ship for his army. Meta Knight attempts to stave off the attack on his ship, but he is preoccupied with King Dedede, who decided to attack at a similar time. Meta Knight loses the battle and vanishes, but Dedede learns of Tabuu and his most devastating attack - the Off Waves, which can reduce many Smashers to trophies in a single long-range attack. Dedede realizes that Tabuu is capable of turning all of the Smashers into trophies at once, rendering no one able to revive anyone, and leaving no one to stop Tabuu's plans. With this in mind, he begins work on an item that can revive a trophy on a timer, without needing a helper's contact, which should make it possible to resist the Army even if everyone is defeated.
Finally, Tabuu sets out to recruit specific Smashers to his cause, using Master Hand as a cover. He focuses his efforts on those who naturally dislike the others, giving him three accomplices willing to help "Master Hand's plan": Bowser, Wario, and Ganondorf. Their objective is to locate and suppress any resistance to the detonation of Subspace Bombs, the weapon developed by the Isle of Ancients to tear pieces of the world into Subspace. To help, the three of them are provided with Dark Cannons: a second newly created weapon, which allows the user to turn any Smasher into a trophy in a single shot. The three accomplices split up to operate in their own ways. Ganondorf remains hidden in an undisclosed location, acting as a liaison with Master Hand and commander for the army as a whole; while he claims to be loyal to Master Hand, he is simply waiting for the right time to overthrow him and take command of the Army himself. Bowser assembles his Koopa Troop and begins to wander the world in search of opponents; he is relatively loyal to Master Hand, but does not care for Ganondorf asserting rank over him. Wario sets off on his own and continues to do whatever he wants, treating his objective as a low priority and not caring at all about the plan or his role in it.
The preparations of Tabuu's plan are complete - he has Subspace Bombs to cut the world apart, an army of goons made of expendable Shadow Bugs to escort the bombs and clear out any opposition, the Halberd to transport said army, and Smasher accomplices with Dark Cannons should more intelligent force be necessary. Finally, the Subspace Gunship is under development and construction within Subspace, which, once complete, will supercede Subspace Bombs and render the operation all but unstoppable.