Notes: Because it is possible to take more than one path in Adventure Mode, there are sometimes two characters' names, divided by slashes when describing a scenario. (i.e.; Peach/Zelda) This means that if you take the first path, the scenario involves the first character, and vice versa. Also, there is no official chapter-by-chapter layout to the actual mode; the following material is divided in to chapters strictly for the sake of clarity.
- The following prologue material is pulled from information in in-game trophies and the Dojo, and is not depicted in in-game video cinematics.
The Subspace Emissary depicts two realms: The "main realm" of "our world", a somewhat typically Earth-based setting known as the World of Trophies, and the realm of Subspace, a world of darkness. The "master" of the world of Trophies is the white glove known as Master Hand; likewise, Tabuu, the main antagonist of the plot, is a blue humanoid figure who is the master of Subspace and is its effective embodiment. Tabuu intends to cut the World of Trophies into pieces and assimilate them into his own world. In preparation for this plot, he has long observed Master Hand and the fighting denizens of the World of Trophies (hereafter referred to as "Smashers"), studying the fighting styles and mechanics of the trophy-based characters. Tabuu himself cannot leave Subspace, so his plan is to gather and arrange an army that Master Hand would lead as his proxy.
Tabuu captures and enslaves Master Hand, and bends him to Tabuu's will using chains of light. Very shortly after acquiring Master Hand, Tabuu learns of the Smasher named Mr. Game & Watch, an individual without any concept of good or evil who, as an entity, is comprised of a trans-dimensional "mass" that has strange qualities. An infinite amount of a primordial substance called Shadow Bugs can be extracted from Mr. Game & Watch, so Tabuu and his puppet Master Hand capture him for themselves. Using the Shadow Bugs, Tabuu creates much of his Subspace Army, the force which he will have his unwilling puppet Master Hand command to invade Master Hand's own world and forward the plot to bring it into Subspace.
The next preparatory phase Tabuu's takes for his goal centers on the Isle of Ancients, a mysterious landmass that floats in the sky above the World of Trophies. Within the floating island is a technologically advanced society comprised of sapient robots classified as R.O.B.s, and up until now they have existed without ever having interacted with those living on the landmass below. All the R.O.B.s are arranged in a simply structured hierarchy: lesser R.O.B.s serving one ruling R.O.B. known as the Master Robot with complete loyalty. They have all lived in peace... until now.
By Tabuu's will, Master Hand directs the Subspace forces to invade the Isle of Ancients and take captive all its denizens. The Master Robot and its R.O.B. brethren are blackmailed into agreeing to serve as the main front of the Subspace offensive; The R.O.B.s thus begin to develop and mass-produce the various armaments and utilities that the Subspace Army would employ, including the Subspace Bombs - timed explosive devices that, upon detonation, would engulf a massive portion of the world into a pocket of Subspace and send that part of the World of Trophies into Tabuu's realm. Each bomb is to be deployed by the Master Robot himself, and to arm each bomb and set its countdown timer, two R.O.B. underlings are to plug themselves into it bomb - R.O.B.s are sacrificed with each detonation of a Subspace Bomb, in other words. The Master Robot, out of shame and sorrow for his decision to serve Tabuu's master plan while simultaneously sealing the fates of his brethren, cloaks himself in a disguise and assumes the identity of the "Ancient Minister".
The Subspace Army, taking the technology from the Isle of Ancients and basing it on the plans for the Subspace Bombs, also begins construction on the Subspace Gunship within Tabuu's realm. This colossal airship can shoot blasts that fully emulate the effects of a detonated Subspace Bomb, and is intended as the Subspace Army's "ultimate weapon" and trump card in its operation. But in order to allow this giant airship to enter the World of Trophies, a massive subspace portal would need to be made.
The captive R.O.B.s furthermore develop personal weapons called Dark Cannons, whose projectiles instantly turn any Smasher into trophy form as though they were defeated and knocked back to the inanimate state by an extremely powerful attack. This emulates an ability Tabuu himself holds within his otherwise fragile wings: a deadly form of energy attack known as Off Waves. The trophification of this world's Smashers is one of Tabuu's goals in his operation, so as to remove any chance of resistance they might mount otherwise. These prized weapons are few in number, though, and they can only be expected to be used properly by Subspace Army affiliates that aren't just single-minded, mass-produced grunts; indeed, Smashers themselves would best be able to use them. So, to bolster the morale and organization of the Subspace Army, Tabuu has Master Hand seek out and recruit Smashers and other high-profile figures within the World of Trophies that would be willing to go along with "Master Hand's" operation to assimilate their world into "his" realm of Subspace. Villainous characters that have had personal conflicts with other Smashers in the past are the ones Master Hand successfully recruit, such as Petey Piranha and Ridley, and the actual Smashers among them are the ones that are given Dark Cannons, signifying their positions as the highest-ranking members and commanders of the Subspace Army: Ganondorf, Bowser, and Wario.
Ganondorf, a powerful, sinister warlock with aspirations for further power and control, swears allegiance to Master Hand in outward appearances only; his real motive is to usurp power from within and take out Master Hand when the time is right. Bowser, a brutish dragon-turtle-like Smasher with his own personal army of grunts and minions named the Koopa Troop, is relatively loyal to Master Hand and likely joins for the sake of settling his long-standing conflict with certain other Smashers, but does not care for Ganondorf. And Wario, a bellicose thug with a penchant for mischief, cares very little for the actual objective he was given and just wants to continue doing whatever he pleases, but he certainly appreciates having a Dark Cannon with which to turn Smashers into trophies. Of course, none of these three Smasher accomplices to Master Hand are aware of Tabuu.
Tabuu's final preparatory motion before his invasion of the World of Trophies is the acquisition of the impressive flying warship named the Halberd, currently owned and piloted by the masked swordsman smasher Meta Knight, as a primary transportation means for the Subspace Army. The Subspace Army launches a violent attack on Meta Knight; Meta Knight attempts to defend, but by complete coincidence this attack transpires at the same time one of Meta Knight's rivals, a penguin-like self-styled "king" among Smashers named Dedede, attacks him. Dedede unknowingly makes it impossible for Meta Knight to repel the Subspace Army's attack, so Meta Knight is forced to flee and give up his ship to the Army, and hide in seclusion elsewhere.
Dedede gets caught up in the Subspace Army's attack on the Halberd, during which he comes to know all about Tabuu, his true nature, and the potential of his Off Waves ability to turn Smashers into trophy form. After managing to flee from the scene, Dedede begins to worry what will happen once all the Smashers of the world are turned into trophies; in this world, a character that has been turned into their respective trophy form from having taken too much damage may be restored to normal should another, active character hit their trophy base. If every Smasher in the world is reverted to trophy form, however, there would be no one left to restore them and each other, and the World of Trophies would effectively end by Tabuu's hand. Thus, Dedede gets to work on developing special brooches named Dedede Brooches, which are set to work on a timer; once set, after a particular stretch of time has elapsed, whichever inanimate Smasher trophy the brooch happens to be attached to would restore that Smasher to normal. Dedede intends to use these Brooches on himself and some Smashers he may find as trophies down the line, so that there is a chance that he and some other Smashers can cheat themselves out of the potential doomsday scenario that could likely happen in the near future.
By this time, the preparation phases of Tabuu's operation is now complete; all of his standing forces and weapons have been assembled, and the Halberd has been prepped to serve as the Subspace Army's frontal flagship and "dropship" - it will deposit payloads of Shadow Bugs onto any area where the Subspace Army is needed to facilitate each of the Ancient Minister's bomb deployments. Acting on Tabuu's will, Master Hand begins the Subspace Army's campaign to invade the World of Trophies, slice it up into pieces, and send its pieces into Tabuu's realm of Subspace. Thus, the Subspace Army begins its campaign.
High up in the sky, at a floating arena named the Midair Stadium; a large crowd is gathered to spectate a competitive one-on-one brawl between two combatants that are sent to the arena in trophy form and take living form: jumping-plumber-turned-celebrity hero Mario and the sphere-shaped, childlike-yet-heroic pink puffball Kirby. Amongst those delightedly spectating from the crowd are two more Smashers, Princesses Zelda and Peach, the latter of whom is closely associated with Mario. Spectators to this match are not limited to the crowd in attendance; floating above the Midair Stadium is an area named Skyworld, which is otherwise uninhabited by Smashers except for a young angel knight named Pit, who cheers by himself while watching the match through the waters of a magic fountain in Skyworld's palace. As the audience watches, Mario and Kirby have their competitive Brawl, and one defeats the other and emerges the victor. In an act of good sportsmanship, the victor soon restores his opponent to living form by hitting his trophy stand base, and the crowd cheers as Mario and Kirby shake hands and wave to the audience. The sky suddenly darkens with red clouds, heralding the arrival of the Halberd, which deposits a payload of Shadow Bugs into the stadium that form into Subspace Army units. Mario and Kirby are quickly joined by Peach and Zelda as they all battle the mysterious invaders; soon, what they perceive to be the leader of the army, the Ancient Minister, floats by and deploys a Subspace Bomb, and it is armed and its 3-minute countdown timer is set by two R.O.B.s that plug themselves into it. The four Smashers barely have time to investigate the bomb when all of a sudden, major Subspace Army member Petey Piranha - a prior enemy to Mario and Peach - appears in the stadium and shoots a cannonball out of his mouth at Mario, blasting Mario off of the stadium and far into the heavens. Petey immediately proceeds to capture Zelda and Peach in individual cages. Kirby must now face the gigantic plant monster and rescue the two princesses alone.
After Kirby defeats Petey, the cages holding the princesses break open. Kirby and the one princess he focused on rescuing first, Zelda/Peach, then watch as another major member of the Subspace Army, the smasher Wario, makes his entrance. Wario points a Dark Cannon at Kirby and Zelda/Peach at first, but then notices Peach/Zelda in her more helpless position and shoots at her instead; a dark arrow that is shot out penetrates the princess' body and instantly turns her into a trophy. Wario grabs the trophy and flees the stadium with all haste, but as Kirby and Zelda/Peach begin to pursue him, Kirby notices that the Subspace Bomb's countdown timer is merely 5 seconds before detonation. Kirby and Zelda/Peach manage to flee Midair Stadium just in time on Kirby's preferred mode of transportation, a Warp Star, just as the bomb detonates and the stadium is engulfed in a Subspace Explosion that sends its area of space to Subspace, leaving an enormous, dark-purple sphere of Subspace behind in its place. Kirby and the princess immediately set off in pursuit of the Halberd.
Back in Skyworld, Pit helplessly watches as the Midair Stadium is consumed by the Subspace explosion. Just then, he is summoned by the goddess of Skyworld, the benevolent Palutena, who grants him the task of combating the Subspace menace and liberating the world. Palutena bestows a magical bow upon Pit to use as his weapon; enthusiastic, Pit gracefully descends from Palutena's palace into the clouds below and begins his journey. Pit very quickly must begin to fight, for the Halberd passes through Skyworld and deposits a payload of Shadow Bugs. Then, Pit spots Mario's trophy, where it has landed since being blasted out of the Midair Stadium by Petey's attack, and revives him. The two team up to fight the Subspace Army and pursue the Halberd through the cloud-like terrain, but they aren't quite fast enough to reach the flying airship. However, a smaller attack ship called an Arwing is seen flying towards the Halberd.
Meanwhile, Kirby and Zelda/Peach have been flying about in search of the Halberd; they are soon surprised to find themselves right in front of it, but seize the opportunity of the moment to make a crash-landing on the battleship's roof. They have only started exploring the ship's roof when the Arwing catches up to the Halberd and engages it in combat; the Arwing is skilled at dodging heavy enemy fire, but only up until the Halberd employs its Combo Cannon, which scores a direct hit. The Arwing is sent spiraling out of control, and as it falls it nearly collides with Zelda/Peach and Kirby. The gust from the near-collision sends the duo falling off the Halberd, and they make a landing at a region of Skyworld named the Sea of Clouds. They briefly explore the Sea of Clouds, and climb down until they make it to solid ground. The two continue their search for the Halberd on foot as they cross through a field.
In a region of jungle far away from Mario and Kirby's respective groups that is the domain of the gorilla Smasher Donkey Kong, he and his monkey nephew, the Smasher Diddy Kong, pursue the Koopa Troop as they try to take back their prized hoard of bananas. After much fighting, the two simians find their stolen bananas, but Bowser himself appears and takes the opportunity to shoot his Dark Cannon at Diddy. Donkey Kong, in a split-second decision, sends Diddy flying away before taking the hit himself. Diddy briefly glimpses Donkey being turned into trophy form as he is sent flying across the jungle, and Bowser claims Donkey Kong's trophy as his prize.
Mario and Pit, meanwhile, have touched down on solid ground into a large plain, and continue their pursuit of the Subspace Army. Eventually, they come across the Ancient Minister himself, but though the two put up a valiant effort, the Ancient Minister still manages to escape.
Elsewhere in the jungle, Diddy swings his way away from where he was saved from Bowser by Donkey Kong, hoping to find help. He soon arrives at a lake, and discovers near the shoreline the smoking wreck of the Arwing that courageously but unsuccessfully engaged the Halberd earlier. Suddenly, out of the lake emerges an immense, serpentine beast, the legendary Pokémon Rayquaza, who is obviously angry with Diddy and the Arwing for invading its territory. Rayquaza blasts the wrecked Arwing with a Dragon Pulse, grabs Diddy, and prepares to finish him off. In the nick of time, the pilot of the destroyed Arwing, Fox McCloud, jumps out of the wreckage and saves Diddy, and the two Smashers team up to defeat Rayquaza together.
Fox is about to head off on his own when he is stopped by Diddy, who tries to convince Fox to help him search for Bowser and try to get back Donkey Kong, and Diddy soon has to resort to literally dragging Fox behind him by his suit's collar. From that point onward, Fox and Diddy travel together and battle Bowser's troops, and they soon encounter what would appear to be the Koopa King himself; strangely, Bowser emits a purple aura, glowing yellow eyes which is his dark form, and is physically larger, and he attacks, but nevertheless, Fox and Diddy defeat him in battle. Diddy and Fox celebrate their victory, but just then, the trophy of Bowser dissolves into shadow bugs, revealing that it was a clone of Bowser comprised of shadow bugs. The real Bowser appears and fires another Dark Cannon shot at them; through quick thinking and reflexes, Fox grabs Diddy and jumps off a nearby cliff, saving them both.
Elsewhere in the World of Trophies, a young, timid boy named Lucas wanders an area that is essentially a deserted, dilapidated zoo. He is suddenly confronted by Subspace Army forces headed by a colossal, animatronic stone statue called the Porky Statue. Lucas attempts to use his physic powers to run from the statue, but he trips and gets trapped. Before Lucas can meet his doom, another psychic child, Ness, heroically appears and topples the statue with his PK Thunder, then shatters it with his PK Flash. The statue reveals itself to be containing the arch-nemesis of both Ness and Lucas, Porky Minch, a misanthropic child their age serving the Subspace Army as one of its major members. Operating from within his personal spider mech, Porky attacks, but Lucas and Ness team up to defeat Porky through an extended battle.
After Porky is finally defeated, Lucas and Ness are then attacked by Wario, who fires his Dark Cannon at Ness repeatedly. After missing several times, Wario aims his weapon at Lucas, and Ness selflessly shoves Lucas out of the way to take the shot for himself. As a frightened Lucas runs away in the pouring rain, Lucas catches a glimpse of Wario holding Ness's trophy and laughing. Lucas soon runs into the taller and more confident Pokémon Trainer, who is in the area seeking Pokémon to catch. Currently, the Pokémon Trainer owns a water turtle Pokémon named Squirtle, and after battling their way through more Subspace forces, the two boys go their separate ways at first. But Lucas, remembering Ness, boldens up and joins the Pokémon Trainer, and the two boys travel together from that point forward.
Elsewhere in the world again, in the middle of a vast, desert-like battlefield, swordsman prince Marth is standing on the balcony of his fortress, watching some R.O.B.s detonate a Subspace Bomb far out in the distance. Marth races to investigate whatever destructive plot is transpiring, but his fortress is besieged by the Subspace Army, forcing him to fight his way through repeated swarms of enemies until he gets to the grounds outside of the fortress. When he reaches the zone of the detonated Subspace Bomb, Meta Knight suddenly flies in and attacks Marth, each momentarily assuming that the other is a member of the Subspace Army. The two duel briefly, but they soon find themselves surrounded by Subspace minions, showing each other very clearly and quickly that they aren't enemies by slashing the minions. The two swordsmen team up to battle and clear out the wave of Subspace Army grunts, and shortly afterward, the they catch sight of the Ancient Minister carrying yet another Subspace Bomb. They desperately try to catch up to him, but are unable to; luckily, out of nowhere, a third fellow swordsman named Ike makes an appearance and attacks with his Aether sword technique, severing the unset bomb from under the Minister and sending the surprised Minister whirling off into the sky. Ike joins the other two to form a swordsman trio, and they immediately resume their pursuit of the Ancient Minister.
By this point, King Dedede has learned that Bowser and Wario have joined the Subspace Army and are turning Smashers into a collection of trophies. With his Dedede Brooch gambit in mind, he decides to start his own trophy collection. On a remote road, he and his Waddle Dee underlings find, subdue, and trophify a lone Smasher, Mario's slightly cowardly brother Luigi by hitting him in the back with his hammer. Just as Dedede finishes this, he sees Wario coming by on his hovering Cargo with the trophies of Peach/Zelda and Ness in tow, and figures this is a perfect opportunity to collect more trophies for himself. Dedede places the Luigi trophy alone on the road to lure Wario, and when Wario tries to collect the apparent freebie he is ambushed and swarmed by Waddle Dees while Dedede takes away the Luigi trophy, steals Wario's Cargo, and drives away with it. Now Dedede has added Wario's previous trophy acquisitions of Ness and Peach/Zelda to his trophy collection, much to Wario's chagrin.
In a thick forest in the southwest region of the World of Trophies, young Hylian warrior and Smasher Link, a close acquaintance of Zelda in the same way as Mario and Peach are associated, comes across a podium while accompanied by a blue fairy he befriended as a child. Set within this podium is the great weapon he was destined to wield in his fight against darkness, the Master Sword, and he draws it out and holds his sword once again. A short time later, Link watches the Halberd pass over the forest's airspace and deposit Subspace Army forces into his area. A sleeping denizen of the forest, the green dinosaur Smasher Yoshi, wakes up to see this as well, and he and Link very quickly decide to team up to fight off Subspace Army goons and pursue the source of the threat, the Halberd.
In a cargo room inside the Halberd itself, the boxes are stacked in an orderly fashion, with the exception of a single, out-of-place cardboard box that is perched on a beam. The box mysteriously stirs.
On the Isle of Ancients, a young woman named Samus Aran, an athletic and capable Smasher even in just her Zero Suit, has infiltrated the floating island through a ventilator shaft and is now sneaking her way into the research facility areas, battling and defeating R.O.B. Squad minions along the way. She soon finds a room where an electric Pokémon Smasher named Pikachu is trapped and held captive in a generator that is cruelly extracting its electric qualities to power the area's machines and technology. Samus breaks Pikachu out of its holding cell with her Plasma Whip, which sets off an alarm and causes many R.O.B. minions to enter the room and attack. The two Smashers team up and battle their way through the facility, and soon find a control room where Samus determines the location of what she has been apparently seeking out in the facility: Her personal Power Suit.
Kirby and Zelda/Peach by now have settled in the shore of another lake following their experience with the Halberd back in Skyworld. Kirby hears a threatening noise in the distance and chases after it, but Zelda/Peach remains behind. Almost immediately, Bowser makes a surprise appearance, and shoots Zelda/Peach with his Dark Cannon and turns her into trophy form. A Shadow Bug clone of Bowser that arrived with him dissolves, swarms over the trophy, then forms itself into a Shadow Bug clone of the princess while Bowser retreats with the original trophy in tow. By this point, Link/Mario and Yoshi/Pit have arrived at the lake shore and are running through the area in their continued pursuit of the Halberd. The clone of Zelda/Peach tries to shoot Link/Mario and Yoshi/Pit with a Dark Cannon, but the weapon is destroyed when Pit/Link, who has also arrived at the lake shore with Mario/Yoshi, slices it in half with his weapon. The Zelda/Peach clone then engages Mario/Link and Pit/Yoshi in combat and is defeated.
Link/Mario stops running, looks up, and sees Mario/Link and Pit/Yoshi standing by the trophy of the fake clone of Zelda/Peach, which disintegrates. To Link's/Mario's eyes, this appears as though Zelda/Peach has been destroyed by the other two Smashers, so in a rage Link/Mario launches an attack against Mario/Link, and their respective companions join the 2-on-2 fray. Link/Mario and Yoshi/Pit are eventually defeated by Mario/Link and Pit/Yoshi and turned into trophies. Just then, King Dedede returns driving his Cargo (Mario/Link briefly glimpses the trophy of Peach/Zelda as part of the Cargo's cargo) to grab the trophies of Link/Mario and Yoshi/Pit with his vehicle's mechanical arm. But Kirby appears from the back of the vehicle (revealing that Dedede's Cargo was the noise he had heard earlier), cuts the arm in half to free the two trophies, and immediately revives them, to Dedede's shock and annoyance. The revived Link/Pit immediately returns thanks by shooting his bow-and-arrow at Dedede's Cargo in an attempt to slow it down, and the two pairs of Smashers seem to immediately forgive each other and join forces to form a five-man band (including Kirby) as they run after Dedede's Cargo as fast as they can, hoping to catch him and get the three trophies in Dedede's possession. They run all the way into and through the first part of a cave complex, and eventually the five heroes glimpse Dedede's castle far in the distance; they see the Halberd appearing to approach it. To reach the castle, they must go through a second cave complex.
In a control room somewhere, Ganondorf, who knows that Dedede and several Smashers' trophies are in the castle below the Halberd's position, transmits the castle's coordinates to Bowser, who acknowledges the order and proceeds to the castle with his Koopa Troop.
At a remote mountain near the ruined zoo, Lucas and the Pokémon Trainer see a dragon-like Pokémon named Charizard fly into a cave, and Lucas tags along as the Pokémon Trainer follows Charizard down a path into an extensive series of ruins that stretch both underground and above ground. Their journey takes them across an active lava pit, and once they cross through back outside, they confront Wario by the entrance to another underground ruin's cave's entrance. Seeing Wario and remembering Ness, Lucas grows bolder and joins the Pokémon Trainer's Squirtle in fighting Wario for the last time. After Wario is defeated and turned into trophy form, Lucas' spirit is uplifted by his victory. But upon remembering Ness, Lucas is distraught to see that the trophy of Ness that Wario originally took is nowhere in sight. Pokémon Trainer cheers him up by suggesting that Ness might be in the next set of cave ruins.
In his personal castle, King Dedede decorates his three trophies - Luigi, Ness and Peach/Zelda - with his Dedede Brooches. He realizes he only has enough Brooches for the three trophies, and though he is dejected that he will have to take off the one he intended for himself to put it on the princess' trophy, he does so, and intends to make another Brooch for himself later. However, at that very moment, Bowser and his troops begin their invasion of the castle. The cement ceiling collapses, and the large blocks of cement that fall to the floor knock Dedede unconscious, seemingly turning him into his trophy form and bury the trophy versions of Luigi and Ness out of sight. Bowser drops through the ceiling and sees the trophy version of Peach/Zelda - the other princess he has been wanting to capture since his capture of Zelda/Peach earlier - and grabs it and runs away from the castle.
By now, Mario, Link, Pit, Yoshi and Kirby clear the second set of cave complexes leading to the castle, and catch up to Bowser. Mario attempts to attack his personal nemesis with a punch, but Bowser forces Mario to miss by holding up Peach/Zelda's trophy as a shield. Pit fires an arrow that Bowser barely dodges, but which makes the Dedede Brooch fall off the trophy of Peach/Zelda. Bowser jumps back and seems to fall backward off a cliff, but it is revealed that below the cliff is where he had parked his personal mode of transportation, the Koopa Clown Car. The Koopa King laughs as he flies off to the Halberd with the princess' trophy in his possession, and Mario and his group are left frustrated. While the other four look upon the Halberd, however, Kirby walks over to the dropped Dedede Brooch, and eats it because he thinks it is food. While all of this is happening, the Ancient Minister and his R.O.B. underlings deploy and set a Subspace Bomb outside of Dedede's castle, and as Ganondorf watches on the display screen in his control chamber, the detonation engulfs the castle (and the trophies of Dedede, Luigi, and Ness inside it are also sent to Subspace). Ganondorf then receives new orders from Master Hand on his display screen.
Back at the underground ruins, the Pokémon Trainer and Lucas continue to explore and fight through Subspace Army minions in search of their respective goals - Lucas searches for Ness' trophy while Pokémon Trainer searches for wild Pokémon to capture and add to his fighting collection. Pokémon Trainer soon encounters and captures the plant-lizard Pokémon Ivysaur, and later he and Lucas team up to defeat and capture the Charizard they saw earlier. The two boys eventually make it into a great underground hall, which for all intents and purposes is a dead-end for them.
Back at the desert-like area, Marth, Ike, and Meta Knight see a colossal, mechanical agent of the Subspace army named Galleom patrolling the desert, and they decide to pursue it through the desert until they catch up to it and engage it in battle. Though Galleom proves to be a fiercely powerful opponent, the swordsmen defeat it nonetheless, but the still-operational beast leaps down a nearby cliff face and lands onto the ground outside the cave ruins. The ground below Galleom collapses under its weight because there is a huge, empty hall right below its position, so it falls down into the ground and ends up at the bottom of the hall which happens to be right where Pokémon Trainer and Lucas are. Galleom immediately attacks the boys in its second battle in a row, but they defeat the robot like the swordsmen did before. Thoroughly weakened, Galleom sets a Subspace Bomb with a 15-second countdown timer hidden within its head as an emergency feature, and grabs the boys and flies upwards out of the hall, out of the ground and into the sky. The Pokémon Trainer has fainted, much to Lucas' despair, but Lucas demonstrates courage by using his own PK Thunder attack to blow apart Galleom's arm and sever themselves from the robot's body. They both enter free fall toward what seems like certain doom, until Meta Knight - who had been watching events unfold from nearby with the other two swordsmen - flies in and catches them both at the last second. Behind them, Galleom's Subspace Bomb detonates in midair next to the mountain containing the ruins, sucking up into Subspace the Wario trophy that was left behind at the mountain's cave entrance. Lucas and the Pokémon Trainer happily share a handshake while accompanied by the three swordsmen, and Marth, Ike, Meta Knight, Pokémon Trainer, and Lucas form a team.
The Ancient Minister, witnessing the detonation of Galleom's Subspace Bomb from a different region of the same desert, exhibits an increasing degree of sorrow over the sacrifices of his R.O.B. brethren that occur whenever they set and detonate such a bomb themselves. He has another Subspace Bomb in tow now, which he is to deploy elsewhere in the desert. After suddenly dodging an arrow shot by Pit, the other four members of his group arrive to resume their chase after the Minister, and the Minister flees while shooting lasers at them. Once again, despite the five-man group's efforts, the Ancient Minister's R.O.B. minions successfully set-up and activate the Subspace Bomb's 3-minute countdown timer, which cannot be stopped however hard the Smashers try. Just as the detonation ensues, one R.O.B. unit waves "good-bye" at the Minister, and all R.O.B. units in the immediate area are sucked into the Subspace explosion and meet their doom. All five of Mario's group barely escape the huge Subspace explosion by relying on their fastest members - Mario rides Yoshi, while Link, Pit, and Kirby hold onto the Warp Star.
Fox and Diddy Kong have been traveling east through the jungle since their last encounter with Bowser, which had ended when they both jumped off a cliff, and they have been battling Subspace Army goons and Bowser's Koopa Troop alike. Eventually, they leave the jungle, but Diddy is suddenly shot in the back and turned into a tropht by Bowser's Dark Cannon blast. A swarm of Shadow Bugs, under Bowser's command, then crawls over Diddy's trophy, then forms a Shadow Bug clone of Diddy. Fox appears to be out-manned and about to be turned into a trophy himself when his fellow Arwing pilot partner, Falco Lombardi, flies in his own Arwing and jumps out to save the day. He kicks the Dark Cannon out of Bowser's hands and destroys it with his two blasters. Frustrated, Bowser flees in his Koopa Clown Car, but the clone of Diddy then absorbs many more Shadow Bugs to grow to three times its size. Fox quickly revives the actual Diddy, and the three team up and battle and destroy the evil clone together.
Falco is about to head off on his own when he is stopped by Diddy, who tries to convince Falco to help him try to get back Donkey Kong, and Diddy soon has to resort to literally dragging Falco behind him by his suit's collar, just like he had done to Fox. Falco, Fox, and Diddy travel together and battle their way through a swamp. When they reach a river that ends in a cliffside waterfall, they eventually see a Smash Skiff with DK's trophy on it fly off towards the Isle of Ancients, visible in the distant sky. Falco calls for support in the form of the Great Fox, Fox and Falco’s co-owned command vessel, so that the three Smashers can fly in the direction of the transport.
Samus and Pikachu continue their exploration through the Isle of the Ancients' research facility in search of Samus's Power Suit, battling their way through more R.O.B. units and Subspace Army grunts. Upon finally reaching the room with the suit, the pair are confronted by two Shadow Bug clones of the Suit, which they dispatch. Soon, Power Suit Samus is back in action, and together she and Pikachu continue their run through the base in search of whoever is leading the R.O.B. units so that they can shut down the base. When they reach a particular dead-end, however, Samus is suddenly assaulted by her arch-nemesis, the dragon-like Ridley and major Subspace Army member, who brutally attacks Samus until Pikachu saves her by attacking Ridley with its Thunder attack. While Samus is fazed from the experience, her power suit is still functional, and she and Pikachu team up against Ridly and successfully defeat him in battle. The two victorious Smashers proceed to exit out of a secret door into the exterior portion of the Isle of Ancients, whereupon they see some R.O.B. units carrying Subspace Bombs out of another part of the base that appears to be a factory for the bombs. Samus and Pikachu decide to reenter the base through that opening.
In another region on the Isle's exterior portion, of the Isle, outside a set of ancient ruins, a little astronaut named Captain Olimar is watching as many small, coloured plantlike creatures he has command over, the Pikmin, attack an oversized R.O.B. unit, but they fail to deal any damage, and many of them are wiped out by the R.O.B.. Olimar is afraid until he looks behind him and sees an extremely fast racing machine piloted by superhero-like bounty hunter Captain Falcon zooming toward his position, and Captain Falcon leaps out of the machine and destroys the R.O.B. with a decisive Falcon Punch. Captain Falcon's show-off moment is spoiled when he accidentally wipes out all but one of Olimar's remaining Pikmin when he lands.
That mishap aside, the two captains decide to team up and fight their way through this area of the Isle, and they soon make it to the floating island’s edge. There, they watch as the Smash Skiff carrying Donkey Kong's trophy approaches the island, and Falco's Arwing flies in, which drops Diddy onto it, who in turn blasts the Subspace grunts occupying the transport and revives Donkey Kong. Seeing their opportunity to help out, Captain Falcon and Olimar jump down onto the skip to introduce themselves to the simians, and not a moment too soon, as more waves of the Subspace Army attack. The four of them join forces to defeat their enemies. The transport then autopilots itself into the interior of the Isle, giving the four Smashers the perfect opportunity to sneak in and strike at the core of the menace from within...
Back in the desert, Meta Knight sees the Halberd engaging in a battle with the Great Fox near a snow-covered mountain. He leaves Marth, Ike, Lucas, and the Pokémon Trainer behind on the ground as he charges his way up the mountain in hopes of catching up to his airship. Along the way, he passes by a pair of mountain-climbing parka-clad children named the Ice Climbers (Popo wears blue, while Nana wears pink) currently hiking up the mountain, and they interpret Meta Knight’s hurried course up the mountain as a challenge. The Ice Climbers put in an effort to get up to the top of the mountain before him, and while both of them have more minions of the Subspace Army to fight through together along the way, they both make it to the summit. Despite working together, the Ice Climbers reach the summit shortly before Meta Knight and cheer for themselves.
Meta Knight encounters an Aura Pokémon named Lucario meditating at the top of the mountain peak, who awakens and challenges Meta Knight to a duel. Meta Knight/Lucario wins the duel, and after he revives Lucario/Meta Knight from his trophy-state, the two shake hands in respect. Just then, the Halberd, which has won its battle with the Great Fox and has it tied underneath itself, rams the Great Fox into the mountain, causing the Ice Climbers to fall to the bottom, but Meta Knight and Lucario manage to jump onto the ship and enter its interior. The Ice Climbers meet up with Marth, Ike, Lucas, and the Pokémon Trainer at the bottom of a mountain canyon, and are threatened by another wave of Subspace Army soldiers, but luckily Mario's five-man group arrives and jumps down to help out the other group. After a long fight, the two teams are left standing victorious.
Inside the Halberd, out of a cardboard box disguise emerges a special forces agent and Smasher codenamed Solid Snake, who had infiltrated the Halberd much earlier for the probable reason that he is trying to combat the menace of the Subspace Army in their own battleship in his own way. As the heavily damaged Great Fox is seen flying away from the Halberd, Snake sneaks through the airship, but quickly hides himself in his box when he hears Meta Knight and Lucario approaching his position. As the other two Smashers pass by, Lucario’s attunement to Aura allows him to sense Snake in the box, and Lucario blows Snake’s cover by lifting up the box. Snake and Meta Knight are just about to fight when Lucario stops them and conveys that the colour of Snake's Aura indicates he is a good character (Lucario's Aura Sight shows Snake's Aura to be coloured a dark blue, while the Primids of the Subspace Army show up as red). With another wave of Subspace Army units on the way to attack them, Snake joins Meta Knight and Lucario in fighting their way through the airship. The three make their way into a room that has Zelda and Peach's captive trophies in cages; almost immediately, Shadow Bugs swarm over the trophies and create Shadow Bug clones of both princesses. After the clones are defeated, the princesses are freed and revived, and Snake tells them to stay put in the room while he and the other two keep looking around.
After Snake, Meta Knight, and Lucario leave, Zelda transforms into her alternate guise, the ninja-like Sheikah Sheik, and she and Peach make their own combat-filled journey through the exterior of the Halberd in spite of Snake's order. They eventually make it to the front deck of the Halberd; at the same time they arrive at that area, Fox, now piloting another Arwing, engages the Halberd again, and destroys one of the airship’s turrets. The explosion from that occurs dangerously close to where Peach is walking, however; Sheik, thinking Fox was shooting at Peach, teleports onto Fox's Arwing and spearhands straight through Fox's cockpit window, forcing Fox to eject out of the Arwing and land onto the Halberd's front deck with Sheik. The two are about to engage in a violent fight when they are stopped by Peach, who offers each of them a cup of tea. Fox is stunned, but realizes that Sheik and Peach aren't his enemies.
In the meantime, Snake, Meta Knight, and Lucario have made it to the Halberd’s main control room, where they discover what appears to be several Mr. Game & Watch copies infesting the place. They send the clones flying through the windows of the control room onto the main deck where Fox and the princesses are, and the clones melt into Shadow Bugs, which merge into a gigantic, immensely powerful mechanical monster named Duon. As Meta Knight stays behind in the control room to regain control of his ship, Snake and Lucario jump out to join Peach, Zelda, and Fox, and Falco jumps out of his Arwing to join the fight as well. The six heroes engage in an intense fight with the monster and eventually defeat it, and the monster melts into Shadow Bugs, leaving behind the trophy of Mr. Game & Watch. Peach revives Mr. Game & Watch and scolds him for the trouble he caused. Mr. Game & Watch feels ashamed for this, so Peach lets him join their group, as Meta Knight retakes his Halberd, causing the Subspace Army to lose their dropship.
Back at the Isle of Ancients, Samus and Pikachu’s infiltration of the Subspace Bomb Factory plays out at the same time as Donkey Kong, Diddy Kong, Captain Falcon, and Captain Olimar’s own infiltration of the Isle’s same factory complex. Thus, the two groups of Smashers cross paths with each other in the final room of the Isle of Ancients - and all six of them are faced with none other than the Ancient Minister himself, the full remnants of the R.O.B. Squad, and hundreds of Subspace Bombs. The Ancient Minister hangs his head as if he is sad, though, and appears entirely unwilling to perform any more detonations, but then a holo-projection of Ganondorf appears and gives the R.O.B. Squad the command to set every bomb in the facility simultaneously. The Minister defiantly stands in the way of his brethren to stop them, but Ganondorf manually controls the enslaved R.O.B.s and have them shoot their former "master", setting his cloak aflame. Then as the R.O.B.s set each bomb, the other Smashers desperately try to stop them and their bombs, but to no avail. As Ganondorf's projected image disappears, he summons the first wave of Subspace Army minions to distract the heroes.
The burning Ancient Minister shoots down some of the enemy forces with his eye lasers, then sheds off his cloak to reveal his true appearance and identity as the master robot named R.O.B., leader of his kind and a Smasher himself. Though he officially joins forces with the other six Smashers in clearing out the entirety of the Subspace minion horde, it becomes all too clear that the detonation of the Subspace Bombs is inevitable. Captain Falcon remotely arranges for his personal flying ship, the Falcon Flyer, to fly into the doomed Isle of Ancients so that everyone may escape from the island in time. Donkey Kong carries R.O.B. with the others as the robot bids a final, sad farewell to the other R.O.B.s. All seven Smashers pile into the ship and fly off toward the isle's exit at full-speed. However, Ridley reappears, now having been reconstructed as a cybernetic version of himself named Meta Ridley, and pursues the Falcon Flyer as it tries to make its escape. The Smashers climb onto the Falcon Flyer's roof and engage Meta Ridley in a high-velocity midair clash in which Meta Ridley makes every attempt to destroy the speeding vessel. They soon manage to defeat Meta Ridley in time to pilot the Falcon Flyer out of the Isle of Ancients. The floating island is soon completely engulfed in a titanic Subspace explosion generated by an enormous group of Subspace bombs set off simultaneously and close together.
In the desert, Mario, Link, Pit, Yoshi, Kirby, Marth, Ike, Lucas, Pokémon Trainer, and the Ice Climbers witness the Isle's Subspace explosion from far off-shore. The Falcon Flyer containing R.O.B., Donkey Kong, Diddy Kong, Samus, Pikachu, Captain Falcon, and Captain Olimar flies in and lands near Mario's group of Smashers, and at the same time the Halberd, containing Meta Knight, Peach, Zelda, Fox, Falco, Lucario, Mr. Game & Watch, and Snake, arrives and lands near the others. The twenty-five Smashers fully acquaint themselves with each other and presumably discuss matters at hand.
The huge Subspace rift left behind by the combined detonation at the Isle of Ancients is large enough to allow the Subspace Army's ultimate weapon through from the other side: the completed Subspace Gunship emerges halfway out of Subspace into the World of Trophies. Indeed, the original purpose of the detonation of so many Subspace Bombs was to open a rift between realms physically large enough to allow the Subspace Gunship through, while discarding the Subspace Bomb Factory at the Isle of Ancients in the process, as there would have been no further use for the factory once the Gunship enters the world. With Ganondorf and Bowser operating the gunship from its top canopy, the Gunship's incredibly large main cannon points toward an area of the ocean off to the side and produces a test-shot, generating a huge Subspace explosion.
Then, Ganondorf and Bowser see the Halberd racing toward the Gunship at full throttle. By Ganondorf's command, the hundreds of enormous turrets lining the Gunship open fire on the Halberd all at once; the Halberd, though able to dodge several of the massive laser shots at first, is completely destroyed by the onslaught. Very quickly, however, the lesser aircraft containing all of the Smashers - the Falcon Flyer, Samus' personal gunship, Fox's Arwing, and Captain Olimar's Hocotate rocket - emerge from the dust cloud and speed toward the portal to Subspace that the Subspace Gunship is currently connected do, skillfully dodging every round of turret fire sent their way. Then Kirby, individually piloting his "personal" ultimate vessel, the Dragoon, flies straight into the Gunship and pierces it, causing the Gunship to begin exploding and disintegrating from the inside. Ganondorf and Bowser must retreat to Subspace, while the Smashers' other five ships manage to enter the portal to Subspace even as the Gunship explodes around them. Now inside the realm of Subspace, the combined force of Smashers - Mario, Peach, Donkey Kong, Diddy Kong, Yoshi, Link, Zelda, Samus, Pit, Ice Climbers, R.O.B., Kirby, Meta Knight, Captain Olimar, Fox, Falco, Captain Falcon, Pikachu, Pokémon Trainer, Lucario, Marth, Ike, Lucas, Mr. Game & Watch, and Snake - begin their exploration of the realm of darkness in search of whoever or whatever is responsible for the Subspace invasion and to put an end to this chaos.
Ganondorf and Bowser are on their way to report to Master Hand, but Ganondorf decides that now is the time to go through with his intended plan to usurp Master Hand's position, so he turns his Dark Cannon on Bowser and shoots him from behind. As Bowser's trophy is left behind, Ganondorf faces Master Hand in person... but immediately sees the chains of light binding Master Hand, and looks upon the puppetmaster Tabuu for the first time - the true orchestrator of the plot to send Master Hand's World of Trophies into Subspace, Tabuu's own realm. Shocked and angered that he has been used by Tabuu the whole time, Ganondorf leaps forward to attack Tabuu, but the incredibly powerful entity turns Ganondorf into trophy form without much effort. The force of the impact of Ganondorf's trophy against Master Hand physically snaps the chains of light off from him, and he falls to the ground free from Tabuu's mind-control. Master Hand regains his composure and immediately and angrily tries to attack Tabuu with all the force he can muster, but due to Tabuu's mighty power, he too is defeated very easily. The force of Smashers finally arrive in time to witness the fallen Master Hand and look upon the master of Subspace. But before they have an opportunity to attack, Tabuu seizes this incredibly convenient opportunity, stretches his wings, and releases his full-powered Off Waves. Every single Smasher is instantly turned into trophies without further incident.
As the Smasher trophies lay scattered and lost within the Subspace realm, Tabuu takes the portions of the World of Trophies that prior Subspace Bomb detonations had sent to his realm, and rearranges them to construct a nightmarish and extensive maze, filled with shadowy versions of Smashers and reincarnations of major Subspace Army members and other monsters (including Ridley, Duon, and even Rayquaza), all of which were created based on detailed analysis carried out by the Subspace Army. The creation and future expansion of this twisted project was apparently Tabuu's ultimate motive in wanting to assimilate the World of Trophies into Subspace, and now with quite literally every Smasher from the World of Trophies turned into trophy form and removed as a threat to his operation, there appears to be nothing else that could possibly stop Tabuu from taking the rest of the World of Trophies for himself.
In the portion of the Subspace Realm currently containing the World of Trophies area containing Dedede's castle, and thus the inanimate trophies of King Dedede, Luigi, and Ness within, the timers within the Dedede Brooches attached to Luigi and Ness reach zero, and suddenly revive the two Smashers. In a moment, they make sense of the circumstances and understand it was King Dedede who caused them to revive, so they revive King Dedede from trophy-form in return. Dedede is ecstatic that his gambit has paid off and is deeply thankful to Ness and Luigi for reviving him, and the three immediately team up and search the rest of Subspace for the trophy of Kirby. After having collected a large portion of the trophies, they reach the area near the entrance to Tabuu's Great Maze where Master Hand lies motionless. King Dedede finds and revives the trophy of Bowser, but Bowser immediately roars and engages Dedede in battle. Dedede defeats Bowser and turns him back into a trophy, then revives Bowser again - and when the ever-so-pompous Bowser roars and tries to confront Dedede again, Dedede smacks Bowser in the face and points him toward the rest of the scene. Bowser takes in the current state of affairs, expresses regret, and begrudgingly allows himself to join Dedede's group.
Elsewhere in Subspace, Kirby is suddenly and spontaneously revived out of trophy state. He spits out what caused him to revive - the Dedede Badge he had inhaled a long while back. Kirby proceeds to set out on his own exploration of Subspace, battling Subspace Army minions and finding and restoring Smasher Trophies along the way. By the time he makes it to the same area that Dedede is in, both Kirby and Dedede have had the potential to collect and restore every Smasher trophy independently. Kirby finds Ganondorf's trophy, but before he can do anything, Bowser physically vents out his anger at Ganondorf's trophy in retaliation for Ganondorf shooting him with a Dark Cannon earlier, then goes into the Great Maze. When Kirby and King Dedede see each other, Dedede happily glomps Kirby and enthusiastically drags Kirby along for the final confrontation in Tabuu's Great Maze.
If Wario's trophy, which had been sucked into Subspace after his last encounter with Lucas at the Ruins in the normal world, was one of the trophies that Kirby revived during his run, Wario will briefly confront Dedede over what Dedede had done to him long ago (when Dedede stole Wario's Cargo and trophy collection), but is taken aback to see that Ness and Luigi - two of the trophies he would have had in his possession had Dedede not stolen them - are in support of Dedede. All three of them point Wario to Tabuu's Great Maze nearby to tell him that they are about to engage Tabuu in a battle to save the World of Trophies; Wario, after a moment of self-reflection, hops on his motorbike and rides straight into the maze to assist all the other Smashers.
In a similar scenario, if Link and Zelda's trophies had been revived during Dedede and Kirby's runs, the two come over to Ganondorf's trophy and agree to revive him; in the past, prior to the Subspace invasion, Link and Zelda had personal conflicts of their own with Ganondorf, but they propose to the newly revived Ganondorf to work with everyone else in the upcoming battle against Tabuu. As the two leave, Ganondorf clenches his fist in frustration over how he was tricked by Tabuu and now must join forces with his two greatest rivals; he does understand that Tabuu is the bigger foe, and puts his personal grudges aside. Thus, the formerly villainous Smashers Bowser, Ganondorf, and Wario join King Dedede, Luigi, Ness, and the other two-dozen-plus Smashers in their greatest challenge yet.
The Smashers enter and explore Tabuu's Great Maze, reliving the many challenges they faced throughout the Subspace invasion of the World of Trophies, while battling the dark versions of the Smashers and the reincarnated major members of the Subspace Army that were all set up to guard the labyrinth. After a lengthy and combat-filled exploration, the thirty-plus heroes finally reach Tabuu. Tabuu immediately spreads his wings and readies a second helping of his Off Waves assault, but all of a sudden, out of nowhere a new hero arrives: an extremely speedy hedgehog named Sonic propels himself straight through Tabuu's wings and shatters them, crippling his trophification ability. The weakened Tabuu proceeds to engage the Smashers in direct combat, and Sonic joins the other heroes in their battle against Tabuu, the most powerful opponent they all have faced. At the end of one final struggle, Tabuu is finally defeated; Tabuu is destroyed, which sends all of the segments of his Great Maze back to their former locations in the World of Trophies, restoring them all back to normal, and all of the Smashers manage to escape back to their world.
And so, Subspace has finally disappeared, the World of Trophies has been saved, and the thirty-plus heroic Smashers stand triumphant on a cliff and share a brilliant sunset. This victory has not been without a heavy price, though: the sheer number of Subspace Bombs involved in the explosion that consumed the Isle of Ancients has prevented that area of space from ever returning to normal despite Subspace having been completely removed, so the Isle is gone forever, and an X-shaped mark of light remains in its place. As of now, R.O.B. will remain the last of his kind. In the last scene, all the characters look at the horizon, where instead of the Isle of the Ancients appears a great luminous cross.