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 and Crazy Hand, the masters of the world. Tabuu captures Master Hand and Crazy Hand with Chains of Light and pulls them into Subspace, giving them 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. Tabuu then captures Pikachu, intending to use its powers of electricity as a power supply for the isle.
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, as well as his second-in-command 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, on the other hand, 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 supersede Subspace Bombs and render the operation all but unstoppable.
A large crowd fills the Midair Stadium for a battle between Mario and Kirby. In addition to the generic crowd, Peach and Zelda are in attendance, and Pit watches from a magical fountain in Skyworld. As one participant defeats the other, the loser reverts to his trophy form; the winner revives him in good sportsmanship and they both wave to the crowd.
An ominous howling noise fills the stadium as the sky is filled with red clouds. The Halberd arrives and drops Shadow Bugs into the stadium, which form into Subspace Army troops. Peach and Zelda join Mario and Kirby as they fight off the invaders. Shortly afterwards, the Ancient Minister appears, dropping a Subspace Bomb that is prepped with two R.O.B.s and set for detonation in three minutes; the Ancient Minister quickly retreats to the Halberd as it begins to depart. As Mario dashes to investigate the bomb, a mysterious smoke cloud appears, and a cannonball is fired from it that propels Mario out of the stadium far into the sky. In the chaos, Peach and Zelda are thrown into individual cages, which are held by Petey Piranha. Only Kirby is left to fight Petey.
Upon breaking one of the cages, Petey explodes in defeat, as Kirby and the princess he freed (Peach/Zelda) jump away. Wario makes an entrance, leaping in from nowhere with his Dark Cannon pointed at Kirby and Peach/Zelda. He prepares to fire, but notices that the other cage has broken and Zelda/Peach is lying outside it, in no condition to evade. Wario turns his Dark Cannon to the easier target and fires, turning Zelda/Peach into a trophy; he quickly grabs the trophy and leaps away. Kirby and Peach/Zelda begin chasing him, but Kirby notices that the Subspace Bomb is about to explode, and summons a Warp Star for the pair to escape on. The Midair Stadium is then consumed by Subspace.
Pit watches from Skyworld as the stadium is sucked into Subspace. He turns away to find Palutena, who provides him with a Palutena Bow and commands him to go and fight the Subspace Army. Pit leaps outside and into the clouds to begin his task. He finds the Halberd quickly; it passes through Skyworld and drops a group of Shadow Bugs that become opponents for him to fight. After some travelling, Pit comes upon Mario. After Pit revives him, Mario teams up with Pit to try and chase down the Halberd, but the pair run out of terrain to traverse, leaving them unable to continue chase. However, an Arwing flies by, which also appears to be pursuing the Halberd.
Kirby and Peach/Zelda also appear to be following the Halberd, though it somehow ends up behind them. Kirby attempts to land on the Halberd's deck, which is more or less successful. Immediately the Arwing catches up, and attempts to fight the Halberd, but the Combo Cannon's arm scores a hit on the Arwing. As it comes crashing down, it flies past the pair, who are then blown off the Halberd. Landing in the Sea of Clouds, the two climb down onto solid ground, fighting the Army throughout, and attempt to pursue the ship on foot.
To the east of the Midair Stadium and Skyworld is a jungle. The Koopa Troop is perpetuating hijinks, carrying a Cargo full of bananas and moving at high speed away from the jungle, where Donkey Kong is attacking the jungle's inhabitants, enraged that his banana hoard has been stolen. As DK spots the Cargo, it fires Bullet Bills at DK, but Diddy Kong appears and shoots them out of the air with his Peanut Popguns. The pair traverse the jungle and through the Koopa Troop to retrieve the bananas. The two eventually find the bananas and dance in happiness, but Bowser then steps into view from behind and prepares to fire his Dark Cannon at the two. DK realizes the setup was a trap and that trying to fight a backed-up Bowser plus an unknown weapon is foolish, so he punches Diddy away from the scene, taking the shot himself. Diddy sees DK get turned into a trophy as he flies away, while Bowser claims DK as a prize. Then the legendary warrior Tara Sachs is shown flying in the area after hearing about the Subspace Bombs. She sees Diddy flying away from DK's punch and flies off to catch him.
Meanwhile, Mario and Pit have come to solid ground and are traversing a plain, continuing their pursuit of the Halberd. When they catch up to the Ancient Minister, he escapes without much effort.
After being caught from his flight, Diddy and Tara move through the jungle searching for help to rescue DK. They finds the crashed Arwing beside a lake and try to investigate when Rayquaza emerges from the lake. Seemingly upset that its territory has been invaded, Rayquaza fires an energy ball at the Arwing, then grabs Diddy and Tara with intent to harm them. Fox then leaps out of the Arwing and frees Tara and Diddy, with the three proceeding to defeat Rayquaza. Afterwards, Diddy physically convinces Fox to join him in trying to save DK, and the three battle through more of the Koopa Troop. Eventually Bowser appears - but with an odd purple aura and glowing yellow eyes. He is defeated, but dissolves into Shadow Bugs as the real Bowser fires a Dark Cannon shot from just out of view, which misses. An enraged Diddy intends to fight Bowser to avenge DK, but Fox and Tara pull Diddy away and escape with him, sharing DK's sentiment about it being too dangerous to fight Bowser.
Far to the south, Lucas is wandering around a deserted zoo. The Subspace Army appears, headed by the Porky Statue, and Lucas runs away in fear. Eventually, Lucas trips over a root and gets his foot stuck under it. He panics, but Ness appears and uses a combination of PK Thunder and PK Flash to attack and destroy the statue. The statue is revealed to have contained Porky Minch and his spiderlike mech. The two psychic boys engage it in battle and defeat it. Shortly thereafter, though, the pair see Wario on top of a pillar. He fires his Dark Cannon at Ness several times, but Ness easily dodges every shot. Wario shrugs and sets his sights on Lucas instead, who is too scared to dodge - so Ness pushes him aside and takes the shot himself. Unconcerned with who exactly he got, Wario walks up to Ness's trophy and laughs while Lucas runs away. Lucas eventually bumps into a Pokémon Trainer that currently has a Squirtle. After the pair fight through more of the zoo, the Trainer heads on his way, while Lucas decides to go with him in an effort to rescue Ness.
To the northwest, the Subspace Army is attacking a fortress that stands in the middle of an ancient battleground. After seeing a Subspace Bomb detonate in the distance, Marth is roused from the fortress and fights his way out to investigate. Upon reaching the blast zone, Meta Knight appears and initiates a swordfight, each assuming the other is with the Army. When both are attacked, they are set straight and team up to cross the battlefield. Eventually they catch sight of the Ancient Minister, who has another bomb ready to be dropped; they fail to reach him, but then Ike appears and uses Aether to damage the bomb and send the Ancient Minister flying erratically into the distance. Now a trio, the swordsmen continue their pursuit of the Army.
By now, King Dedede has realized that the enemy (Bowser & Wario) is collecting the trophies of defeated Smashers and taking them away so they cannot be revived. He decides to start his own collection, which he plans to keep safe with his brooches. He starts his collection by ambushing Luigi on a dirt road and turning him into a trophy. Seemingly knowing that someone is approaching, he hides alongside his army of Waddle Dees while leaving Luigi's trophy on the road as bait. Indeed, Wario rides up the road on his Cargo carrying Zelda/Peach and Ness. Seeing a free Luigi on the road, he pulls over, takes the trophy, and laughs. Distracted, he is then ambushed by the Waddle Dee Army. Dedede then takes Luigi, tosses him onto the Cargo, and drives away with it and all of the trophies. As the Waddle Dees follow Dedede, Wario gets up and yells at them in anger and frustration.
In a forest to the southwest, Link finds the Master Sword in a pedestal and draws it. He passes by Yoshi, who is asleep on a large tree stump. As the Halberd passes overhead and deploys Shadow Bugs, the two team up and fight through the forest in pursuit of the ship. Meanwhile, a cardboard box on the Halberd is seen moving and fidgeting.
Inside the Isle of Ancients' research facility, Zero Suit Samus has snuck inside and is wandering around while fighting Subspace Army minions and parts of the R.O.B. Squad. She finds some sort of generator holding a Pikachucaptive, and breaks it to release it; the pair continue to move through the complex. After a while, they find a control room, which lets Samus see the room where the Power Suit is being held.
Kirby and Peach/Zelda have reached the shore of the western lake. Kirby spots something and rushes off in pursuit, leaving Peach/Zelda behind, who is ambushed by Bowser and shot by his Dark Cannon. A waiting Shadow Bug clone of Bowser uses the defeated trophy to change into a clone of Peach/Zelda while he sneaks off with the real one. By this time, Mario/Link and Pit/Yoshi have also reached the shore in pursuit of the Halberd. The Peach/Zelda clone attempts to use the Dark Cannon that Bowser left behind to fire at them, but Link/Pit and Yoshi/Mario have also arrived, destroying the weapon in one slash. The two Smashers then fight the clone and destroy it. However, Mario/Link has noticed the fight from a distance, and believes that Peach/Zelda has been attacked and defeated, so he attacks the pair in rage as his partner joins in. Once the two-on-two fight finishes, before the winners can revive the losers, King Dedede drives by and snatches the two defeated Smashers with the Cargo's arm. Link/Mario manage to see that Zelda/Peach's trophy is aboard the Cargo as Dedede drives away. Dedede then realizes that Kirby has snuck onboard the Cargo (due to spotting it earlier). Kirby uses Final Cutter to cut the arm and release the two trophies, and quickly revives them before they hit the ground. Irritated, Dedede turns the Cargo around and begins to flee, but the revived Pit/Link nails it in the nose with an arrow. The five Smashers join together and chase the damaged Cargo, assuming that, like the other antagonist Smashers, Dedede is collecting trophies to hide them away so they cannot be revived. Seeing the busted Cargo at the entrance of a set of caves, the group heads inside and fight through the Subspace Army and Koopa Troop to see a castle in the distance, with the Halberd hovering overhead.
Ganondorf, in his undisclosed location, has become aware that Dedede is planning something and is hoarding trophies in his castle. He transmits this information to Bowser, who sets off to ambush the castle.
To the east of the ruined zoo, Lucas and the Pokémon Trainer see a wild Charizard fly towards a cluster of ruins; as the Trainer is seeking a Charizard, the pair head down the path to the ruins. Upon going through a cave and back outside, they run into Wario again. Remembering what happened to Ness, Lucas decides to get revenge and fights Wario alongside the Pokémon Trainer. Wario is defeated and transformed into a trophy. Lucas and the Pokémon Trainer are ecstatic at first, but Lucas is then saddened because Ness is nowhere in sight; the Trainer suggests he could be in the remainder of the ruins.
In his castle, King Dedede has his collection of three trophies - Ness, Luigi, and Zelda/Peach. He applies his Dedede Brooches to the first two, but runs out of them; he decides to use the one he was saving for himself on the princess, planning to make some more later. However, the Koopa Troop attacks, and the ceiling caves in, dropping a large chunk on Dedede's head and knocking him out ( eventually he becomes a trophy). The cave-in also leaves Luigi, Ness, and Dedede covered in rubble, so when Bowser and the Koopa Troop glance around, they only spot the Zelda/Peach trophy to take.
Mario, Pit, Link, Yoshi and Kirby's group also reaches the castle. Seeing nothing but a hole in the wall, they traverse a second set of caves and catch up to Bowser. Mario attempts to get the jump on him, but he uses the princess as a shield, neutering the attack. Pit quickly fires an arrow that Bowser successfully dodges, which causes the Dedede Brooch to fly off the princess and Bowser to fall off a cliff - though he lands directly in his Koopa Clown Car, and escapes to the Halberd. While Kirby inspects the Dedede Brooch, the Ancient Minister detonates a Subspace Bomb that engulfs Dedede's castle. Ganondorf observes the castle get swallowed by Subspace just before a new message comes in from Master Hand.
Back in the ruins, Lucas and the Pokémon Trainer continue to fight through the cavernous constructs - during which the Trainer captures a trophyized wild Ivysaur and battles the previously seen Charizard, capturing it too. The duo then wind up at a dead end.
Meta Knight, Marth, and Ike have progressed eastward across the desert to the east of the battlefield. Having lost the Ancient Minister, they find Galleom in his tank form cruising across the desert, and decide to follow it. Upon catching up, the swordsmen defeat Galleom in battle, who leaps off a cliff and crashes into the ruins right next to Wario's trophy - and into the room that Lucas and the Pokémon Trainer have entered. Galleom attacks for its second battle in a row, but is defeated again. Instead of simply falling apart, Galleom grabs hold of its opponents and propels itself skywards, activating a 15-second countdown on a Subspace Bomb embedded in his head. Seeing the Trainer has fainted, Lucas gains a sudden confidence boost and uses PK Thunder to break off Galleom's arm, freeing the two, but sending them falling towards the ground. Lucas holds the Trainer as they fall to their doom, but the two are then quickly caught by Meta Knight, who carries them away to Marth and Ike's location while Galleom's Subspace Bomb detonates in midair, barely reaching the ground and sucking up Wario's trophy. Upon landing, the Trainer regains consciousness, and shakes Lucas' hand.
The Ancient Minister watches Galleom's Subspace Bomb from back in the desert and exhibits an increasing degree of sorrow over how R.O.B.s must be sacrificed for each bomb. He is roused by one of Pit's arrows, which he dodges as the group resumes their chase. After a short while the Ancient Minister deploys the bomb he was carrying, which the Smashers fail to stop, and so must escape as several nearby R.O.B.s are destroyed.
Diddy Kong, Fox and Tara continue to travel east through the jungle and reach a more swamp-like area. As they move on, Bowser successfully nails Diddy with a Dark Cannon shot from a distance, he fires at Fox and Tara, but they dodged, Bowser and sends in a troop of Shadow Bugs to clone him. Much to Tara's horror. Fox and Tara is about to face a two-on-two when Falco shows up, punts the Dark Cannon out of Bowser's hands, and destroys it with two Blasters. Bowser is displeased and leaves in his Clown Car, but first commands many more Shadow Bugs to merge with the existing Diddy clone, rendering it significantly larger and stronger. Fox revives the real Diddy, who is shocked by the humongous clone. Together with Falco, they defeat the imposter. Diddy then physically convinces Falco to join them in their goal of saving DK, and the quartet continue through the swamp. Upon reaching a cliffside waterfall, they spot the Smash Skiff, which takes off towards the Isle of Ancients with DK's trophy on board. Diddy grunts in anger thinking the chase cannot continue, but Falco has a plan and summons the Great Fox.
Samus and Pikachu continue through the research facility. Upon reaching the room with the Power Suit, two Shadow Bug clones of it appear. The pair defeats the fakes, and Samus suits up as they continue to move through the facility. Suddenly, Ridley appears and bashes Samus against the wall. Pikachu attacks Ridley and frees Samus with Thunder. Although Samus is hurt, she and Pikachu fight and defeat Ridley. Afterwards, they find an exit to the Isle of Ancients' surface, alongside another exit with R.O.B.s carrying Subspace Bombs out of it. They decide to enter it.
Elsewhere on the Isle's surface, near a different set of ruins, Olimar is attempting to topple a giant R.O.B. with a horde of Pikmin. The R.O.B. awakes and shakes all the Pikmin off, killing most of them. Olimar backs away in fear as a red Pikmin points to the Blue Falconscreaming in from the distance. Captain Falcon erupts from it as he delivers a Falcon Punch to the robot's head, easily knocking it over - and killing all but one of the remaining Pikmin. Despite this, the two captains team up and make their way towards the edge of the island, where they see the Smash Skiff with DK on it coming in. An Arwing flies overhead and drops Diddy and Tara (hanging onto outside of it) onto the transport, who knock off all the Army members currently onboard, Falcon picks up a terrified Olimar and leaps off the island, landing on the Skiff as Diddy revives DK - who easily breaks free of his chains and is ready to fight alongside the other three as troops try to protect the transport. After the enemies are defeated, Falco signals success and flies elsewhere with Diddy waving goodbye and thank you. The Skiff continues its programmed course into a hangar of some sort into the isle.
It appears that the Great Fox has been directed into combat with the Halberd as some sort of distraction - the two ships are firing incessant blasts at each other. The battle is taking place close to the top of a snowy mountain. Meta Knight sees a chance to reclaim his ship, and abandons his group to begin ascent. He passes the Ice Climbers on the way up, who take his quick speed as a challenge, and the new group fight upwards to reach the summit. Upon reaching the top, a Lucario is found meditating on the peak. It leaps towards Meta Knight and challenges him to a battle; the winner revives the loser as they shake hands in respect. Just then, the Halberd plunges through the clouds grabbing the Great Fox with its Combo Cannon, ramming it into the mountain and knocking the Ice Climbers off. Meta Knight and Lucario manage to use this opportunity to jump onboard. The Ice Climbers land by a canyon next to the Marth/Ike/Lucas/Pokémon Trainer group as the Halberd drops a crowd of Shadow Bugs; Mario, Pit, Link, Yoshi and Kirby's group arrives just as the fight starts, and Mario, Pit, Link, Yoshi and Kirby's group merges with Lucas, Pokémon Trainer, Ice Climbers, Marth and Ike' group soon after. Tara's friends, Anna and Capucine make their debut and are showing flying in the cold air, looking for Tara. they find the Halberd and aboard it.
Inside the Halberd, Snake decides the time is right, and leaves his cover to begin operations as the damaged Great Fox limps off. He hides in a box upon hearing footsteps, but is shocked to be exposed by Lucario, who notices him due to his aura. A leery Meta Knight is told by Lucario that he is an ally. They even ran into Anna and Capucine. They join them. The quartet continue to fight through the Halberd to find what appears to be a cargo bay, with both Peach's and Zelda's trophies in cages; both princesses are cloned by Shadow Bugs, and are summarily defeated. Peach and Zelda are freed and revived, though Snake tells them to stay put while his group moves off.
As soon as Snake, Meta Knight and Lucario's group leaves, Zelda takes on the persona of Sheik and sets out on her own journey, with an amused Peach, Anna and Capucine following. The two fight around the Halberd's exterior areas to reach the top deck. Fox is back in another Arwing, and is attempting to destroy the Combo Cannon, which, due to how close the princesses were to it, makes Sheik think he is shooting at them. Sheik teleports onto the Arwing and breaks the window, forcing Fox to eject and land on the Halberd. As Sheik and Fox are about to fight, Peach offers the two some tea, which brings the conflict to an abrupt (and confusing) end.
In the meantime, Meta Knight, Lucario, and Snake have reached the Halberd's bridge. They find that the ship is being run by several clones of Mr. Game & Watch. Snake runs in and busts all the clones out the window, where they land on the deck beside Peach, Zelda, and Fox. Almost immediately, the clones all dissolve into Shadow Bugs and merge into Duon. As Meta Knight remains on the bridge to take control of the ship, Snake and Lucario jump down to help in the fight, in addition to Falco who arrives just in time. Once Duon is defeated, it leaves Mr. Game & Watch's trophy behind; once revived, he joins the group. The Subspace Army has now lost its dropship.
As Samus and Pikachu fight through the Isle of Ancients' Subspace Bomb Factory from above, Donkey Kong, Diddy Kong, Captain Falcon, Tara and Olimar fight through from below. The six of them meet in what appears to be a storage room, containing dozens of bombs - in addition to the R.O.B. Squad and the Ancient Minister, who appears dejected and has no apparent interest in fighting, much to the Smashers' surprise. Ganondorf rings in as a hologram and commands the R.O.B. Squad to detonate all remaining Subspace Bombs immediately - the Subspace Gunship has been completed, and a rift large enough to allow it entry into the world is necessary, even if it means the destruction of the bomb factory and the Isle of Ancients as a result. The Ancient Minister has had enough; he had only allowed the sacrifice of two per bomb to keep the rest alive, so he commands the confused R.O.B.s to ignore the order. Ganondorf activates some sort of override that causes the R.O.B.s to not only begin preparing the bombs but also open fire on the Ancient Minister, setting his cloak on fire. Ganondorf cuts the communication as he sends in a wave of troops to distract the Smashers, who had been attempting to disrupt the bombs' deployment. As Ganondorf cackles evily, Tara sobs in misery over the suicide attack as she pulls on A R.O.B in anger and fear.
The burning Ancient Minister takes out some of the enemy forces with his Robo Beams and throws off the remains of his cloak to reveal to the other Smashers that he is a R.O.B. himself, and joins them in combating the Subspace Army troops. Once the enemies are defeated however, they realize there remains no way to stop the Subspace Bombs from detonating. Believing his race's elimination is inevitable, R.O.B. manages to send all the other R.O.B.s into some sort of sleep mode, including himself; DK will have none of it as he carries R.O.B. out of the room, with the group racing to escape the Isle of Ancients and board the Falcon Flyer that Falcon has remotely summoned. After the group reaches and boards the Flyer, Meta Ridley appears, determined to delay or destroy the ship before it can escape the blast zone. The Smashers battle Meta Ridley on the Flyer's roof and are victorious, escaping the Isle of Ancients before it becomes entirely engulfed in Subspace.
From the mainland shore, the group of Smashers that had fought at the canyon watch the Isle of Ancients vanish. They are joined by the Falcon Flyer and the Halberd, forming a force of twenty-nine. Tara is reunited with Capucine and Anna.
The Subspace Gunship emerges from where the Isle of Ancients used to be and fires a shot of its main cannon into the distance, rendering an enormous patch of unused ocean into a Subspace detonation. Capucine and Anna fly over to fight, almsot forgetting to bring Tara with them. Bowser and Ganondorf are perched on the ship's command platform overseeing the test. The Halberd is then seen approaching from the distance. Knowing the Halberd has been taken over by the other Smashers, Ganondorf orders the Gunship to open fire with its primary turrets. It does not take long for the Halberd to be destroyed, but the Falcon Flyer, Samus's gunship, an Arwing, and the Hocotate Ship fly out of the wreckage and continue advancing. Tara watches from the beach in tears over how amazing the battle is going. Ganondorf commands the secondary weapons to also fire, but none of them can land a hit on the smaller craft. Kirby then arrives riding the Dragoon from a different direction, suggesting the Halberd and the other ships were a distraction, and flies it directly though part of the Subspace Gunship's cannon. The entire Gunship begins to explode as Bowser and Ganondorf retreat into Subspace, while the Smashers fly their ships inside and begin their campaign to fight through the Subspace Army and find out a way to stop them. At the beach, Tara sees no other choice and flies into the subspace with everyone else.
As the Smashers progress through Subspace, Bowser and Ganondorf are due to meet with Master Hand. Before he appears, Ganondorf decides now is the time to take over, and fires upon Bowser with a Dark Cannon. Kicking Bowser's trophy off to the side, Ganondorf meets Master Hand and Crazy Hand - and sees the Chains of Light for the first time, connecting him to Tabuu. Upset that he has been fooled the whole time, Ganondorf attempts to attack Tabuu, but his offensive is easily blocked. As Ganondorf falls back to the ground and becomes a trophy, he collides with Master Hand and Crazy Hand, breaking them free from the Chains of Light and from Tabuu's control. Now free, Master Hand and Crazy Hand also attempted to attack Tabuu, but also fails to accomplish anything, being knocked back to the ground by Tabuu with little effort and lying still, seemingly dead. At this point, the Smashers arrive and realize what is going on, only for Tabuu to unleash his Off Waves and defeat all of them. As Tabuu unleased is Off Waves, Tara activates her teleportation spell to bring everyone with her, But Tabuu's attack incapacitates most of her spell, only allowing her to save herself. With no more Smashers around, Tabuu begins assembling The Great Maze out of the colonies created by the Subspace Bombs, and fills it with the remnants of the Subspace Army plus subspacial clones of the Smashers and the bosses they had previously defeated.
In the colony containing King Dedede's castle, Tara appears from her incapacitated teleportation spell, She breaks down in tears after using her sixth sense to witness what Tabuu has done. Her attention turns to Luigi, Ness and King Dedede as trophies. She goes over to them to revive them, but stops in curiosity over the sight of the Dedede Brooches. The Dedede Brooches activate, reviving Luigi and Ness. Ness connects the brooches with Dedede's trophy and deduces that he is the reason for their revival, King Dedede's own brooch on him revives himself. His plan successful, Dedede hugs them in elation. As he teams up with the other three, Tara witnesses the whole thing and hugs all three of them in happiness, thanking Dedede for making brooches to revive the victims of Tabuu's attack. The four begin to cross Subspace towards the Great Maze, reviving all the Smashers they find along the way (In order: Samus, Pit, Falco, Lucas, Ike, Donkey Kong, Pokémon Trainer, Pikachu, Marth, Olimar, Fox, Mr. Game & Watch, Diddy Kong, Captain Falcon and Mario.). Upon reaching the staircase at the Great Maze's entrance and seeing Bowser lying there, they revive him as well, only for him to attack Dedede. Dedede wins the subsequent fight and revives Bowser again; Bowser tries to start another fight but is flicked in the face by Dedede, who directs Bowser to Master Hand's motionless form. Bowser begrudgingly decides to join the group to get revenge on Tabuu.
At the same time, Kirby is revived, having eaten the Dedede Brooch that had fallen off the princess Dedede had collected. Kirby sets out across Subspace and collects the rest of the Smashers that Dedede's group had not come across (In order: Peach, Zelda, Meta Knight, Link, Yoshi, Lucario, R.O.B., Ice Climbers, Snake and Wario.). Kirby reaches Ganondorf's trophy, but Bowser shows up and vents his rage on it as revenge for Ganondorf shooting him with a Dark Cannon, giving Kirby second thoughts about getting near it. Dedede then appears, hugs Kirby, and drags him along towards the Great Maze.
Link and Zelda have come upon Ganondorf's trophy, and agree to revive him. Directed to the Great Maze, Ganondorf is averse to join forces with his two biggest enemies. Nevertheless, he sees that Tabuu is the bigger foe, and infuriated that he had been manipulated, he agrees to help.
After Tara, Capucine and Anna have revived Diddy Kong, he sees Bowser and runs to him to get back at him for turning DK into a trophy before, but Tara stops him, directing him to the Great Maze, Diddy softens up, knowing that Bowser has had been manipulated the whole time and the four enter the maze.
Finally, as the Smashers are preparing to enter the Great Maze, the revived Wario shows up, boots Dedede in the head as revenge for stealing his Cargo and trophies, and has a laugh over it. Seeing that two of said trophies (Luigi and Ness) are on Dedede's team surprises him enough to stop fooling around. Wario is then offered to join the group; after a bit of reflection, he agrees, and rides his bike up the stairs to the entrance. Tara uses her hologram scanner and explain the Maze they'll be going through in order to get to Tabuu. After that, everyone heads up towards the stairs for their big battle against Tabuu.
The thirty-eight Smashers enter the Great Maze. After a lengthy and combat-filled trek, they finally reach the center and break all the seals guarding the final door to Tabuu's residence. Tabuu attempts to use another set of Off Waves against them. As Tara desperatly tries to find a spell in her spell book to counter it with this time; no help from the brooches, Sonic appears and damages his wings, rendering the attack unable to decimate the entire group at once. Tara turns into her Rainbow Etoile form and confidently ventures out forth to brutally battle Tabbu herself. Thus, Tabuu faces the three dozen Smashers in the final battle, and is ultimately defeated by everyone including Tara herself using her own staff to launch a devasating attack.. All the colonies composing the Great Maze are restored to their rightful positions in the real world, with the Subspace detonations all being sealed off. However, the amount of Subspace Bombs simultaneously detonated on the Isle of Ancients has ruined the isle's ability to return to real space - it is claimed to be destroyed forever. Instead, there is a giant X of light in its place. The Smashers manage to escape to their world. All thrity-eight are excited over Tabbu's defeat. Tara is shown in tears of joy and happiness with a overly happy Diddy Kong.