One lonely night in the Beanbean Kingdom, two Bean folk come across a strange black orb growing in the middle of the fields outside Castle Town.
The next day, Alex catches the news of this orb and decides to go check it out, especially upon suggestions that Gemini will be there waiting for him.
Upon arriving in Beanbean Fields Alex meets up with a Koopa reporter named Kaylie, who directs him towards Gemini.
Gemini and Kayle seem to be familiar with each other but Gemini threatens Alex not to press him further on the connection. After a bit of time spent examining the orb a Primid starts to emerge, so Alex is able to identify the orb as a Subspace Orb.
Gemini takes to fighting the Primid variants until they pull back to summon a new type of Greap known as the Death Greap.
Gemini activates his Demon Form to finish it off and for the time being, the Subspace Army relents. Gemini decides to report back to Alpha, smoothly evading an interview with the antsy Kaylie.
Alex heads back as well, receiving a note telling him to meet up with Mario, Luigi and Driad at E. Gadd's lab. There, Mario explains what's going on to everyone.
He recalls the events of Smash Bros. 64, Melee, and Brawl, specifically the Subspace Emissary in the latter. After he's done going through in such excruciating detail, the group is teleported to Alpha's Command Sphere, reuniting with the Goomba and Koopa.
Alpha exposits that thanks to his men's efforts, they currently know where the remaining Subspace orbs are going to pop up around the planet.
One will appear in Star Haven, another in Toad Town, one outside the M.S.I. Base itself, and another outside Koopa Village.
Upon hearing that last one Gemini suddenly freaks out and abandons his post. Though Alpha tries to stop him, Gemini states that "Gemini is not disobeying this order", and Alpha lets him go.
The rest are divided up as such: Mario, Luigi and later Mallow will protect Toad Town. E. Gadd, Driad and Alpha will handle the one outside the base. Alex will be sent to Star Haven. Eventually they hope to give Alex an opening to go in and fight the reborn Tabuu.
Once everyone splits up, the battle for the planet begins in earnest.
Gemini is the first to arrive at his location and quickly rallies the Koopas and Bob-ombs together to make their stand against the Subspace Army.
Many new foes arrive to carry out their master's will, but thanks to Gemini's leadership the group is able to keep the village safe for a time.
But soon the numbers continue to flood out of the orb and start overwhelming the villagers. Its around this point that Kooper makes a sudden appearance, quickly recognizing Gemini as an old friend and playfully bantering with him about not making a call.
Gemini smiles and together with Kooper the two friends tear their way through the Subspace Army until the orb spits out one of its newest generals, a giant Greap by the name of the Greap Juggernaut.
The Greap effortlessly powers through Bombette and Kooper's strongest efforts and even pins down Gemini in his Demon Form.
When the creature taunts Gemini for trying to resist the assimilation of his master, Gemini erupts into his Star Spirit powered form and quickly slices the Greap down.
Then, as Kayle recognizes him as an old flame and friend, Gemini reassures her with the spread of his angelic wings and stands alone against the incoming tidal wave of Subspace foes.
He vows to destroy the entire army alone without a single scratch coming to his home. Today he fights not as Gemini of the Blood Thunder, but Koopis, a Koopa from this village.
So alone he charges on against a relentless, devouring horde.
Meanwhile, Alpha and Driad prepare to fight the Subspace Army while E. Gadd mans the Command Sphere's mobile weapons' system.
Alpha immediately assumes the Star Spirits' power while Driad simply goes into Wolf Form for now. They sweep their way across the battlefield and use their partnership to their best advantage to cut down the swathe's of enemies before them, while E. Gadd provides cover fire.
Eventually the Subspace Orb spits out one of Tabuu's commanders, Duon, reborn in a new, stronger body.
Driad uses the Star Spirits' power too and joins Alpha in taking the creature down. Thanks to some heavenly intervention from E. Gadd firing off a Holy Hand Grenade, Alpha is able to hijack the robot's systems and convert it to his side for now.
With Driad comfortably holding the front line, Alpha rides Duon into Subspace to go assist one of the other parties in their battle.
Alex and Geno are the sole fighters gathered before Star Haven and the invading Subspace Army. Alex plays around as the army poses little threat to him, not even bothering to go into his elemental forms and showing a stunning display of cockiness.
Eventually Galleom emerges, also reborn with a stronger body. When he struggles to do anything to Geno, let alone Alex, he suddenly receives a massive power boost from a certain witch and manages to put Geno on the ropes.
Alex goes to intervene but even starts having trouble, and the Subspace Army is allowed to advance towards Star Haven.
Suddenly, the invading forces are sliced through by Duon's beams, thanks to Alpha's sudden intervention. Alpha takes the fight to Galleom with Geno's help and tells Alex that now's the time to go in and take the fight to Tabuu.
Alex nods and dives into Subspace.
But there's still one last fight in Toad Town. After having Peach and the residents of Toad Town retreat to a bunker, Mario, Luigi and Mallow prepare to fight.
As expected the Subspace Army alone can't match the three using their Star Spirit powers, so the orb spits out another new General, by fusing a ton of Spaaks together to create a djinn by the name of "Shock-Gra-La".
Then, when that's not enough, the orb spits out a Giga Bytan to get in Luigi's way. And even THEN the orb keeps pumping out new, large threats to keep the three preoccupied.
Its clear this orb is of great significance, being at the center of the strange formation. And that significance becomes all the more apparent when, with a planet-shaking roar, a dragon begins to pull itself free from the Subspace orb.
Its presence comes as an ill omen for the planet's safety, with Mario and Luigi barely able to put a dent in the beast.
However, the timely arrive of Bowser and his kids gives Mario and Luigi a chance to go into the orb itself to confront Tabuu. Bowser refuses to surrender HIS kingdom to some glowing blue man and proceeds to pound the dragon in the snout, slowing its advance.
Mario and Luigi meet up with Alex in Subspace and, after getting each other up to date, continue on to try and find Tabuu.
However, Mario and Luigi are suddenly warped away to another location to fight their dark trophy counterpoints, leaving Alex to stand before Tabuu.
Tabuu has also been reborn, now black and white, as Twilight Tabuu, the Sunset of all Worlds.
Tabuu shows disdain towards Elemental Overlord's and attacks him. Alex fends him off, forced into his Conduit Forms and later, Phoenix Form, just to stand a chance against the lord of Subspace's surprising might.
But during this battle Tabuu senses the boy's curiosity and decides to divulge just why he's so desperate to attack the Mushroom Kingdom, and why he launched his first Subspace attack in the World of Trophies.
Tabuu was once a brilliant scientist studying interdimensional travel on the Isle of the Ancients. But one day, without warning, Master Hand attacked and wiped out his people in one fell swoop.
In desperation Tabuu tried to use his researched to create a tear in the dimensions that would eliminate the Master Hand...Only for the tear to swallow him whole into a new realm known as "Subspace".
There Tabuu became swallowed up by its energies and reborn as the blue man Mario and company recognized in the past. Now, no longer able to interact with the physical world, he planned his revenge.
He manipulated the R.O.B.s and Mr. Game and Watch to do his bidding, crafting Subspace Bombs so his Subspace would spread throughout the Master Hand's World of Trophies.
His plan was to assimilate the parts of the world through Subspace to evolve and become strong enough to permanently kill the Master Hand, for as he dreadfully discovered the Master Hand could only be temporarily stopped.
But Sonic the Hedgehog foiled his plans at the last second, and he seemingly died.
However, he found himself revived all of a sudden, and granted the capacity to take his revenge upon the Master Hand by assimilating the entirety of Plit.
When the dragon pulls itself through the Subspace Orb, Subspace will expand over the entire planet, and that will allow Tabuu the ability to continue consuming planet after planet in Subspace to increase his power.
As to why he hates the Elemental Overlord...
Its because he stood by and did nothing while his planet was attacked by Master Hand, that he despises him.
Alex thinks this is stupid and that this revenge will get a lot of people killed. Tabuu doesn't care at this point. He lives literally only because of revenge. If he surrenders his hatred, he'll die having done nothing.
Alex meets Tabuu's hatred head-on and vows to take revenge on the Master Hand for him. But Tabuu sees little reason to believe empty words, and continues to fight him.
Alex nevertheless proves the strength of his determination to Tabuu, and Tabuu decides to let go of his hatred at long last, sacrificing himself to seal off Subspace forever.
In the aftermath of the battle, Gemini rests in his friend's arms, while Driad and Geno lick their wounds and clean up the remaining Subspace Army.
Alpha, however, stares at the deactivated Duon and Galleom and sees them as a way to keep Alex in check if he were to go rogue...
Alex returns to the Mushroom Kingdom and creates a grave for Tabuu on the outskirts of town. He brings R.O.B. with him to say some final words to the former lord of Subspace.
...And that's the end of that.
End of Special 1.