List of cutscenes in the Subspace Emissary
 List of cutscenes in the order they appear
 The World of Trophies
The camera descends on Midair Stadium, where a large crowd, including Peach and Zelda, are observing the stadium. Mario and Kirby are launched into the stadium for a friendly fight, and their trophies are revived, beginning the fight.
 Pit Watches from Above
 Mario/Kirby Beats Kirby/Mario
Mario/Kirby has won the match, but quickly revives Kirby/Mario.
 Attack On the Stadium
As Mario and Kirby wave to the crowd, the sky suddenly turns red and the Halberd flies in to drop Shadow Bugs into the stadium, which quickly form Primids. Peach and Zelda notice this, and they rush over to help Mario and Kirby ward off the Primid hoard.
 The Ancient Minister and the Subspace Bomb
After the Primids are defeated, the Ancient Minister flies into the stadium and drops a Subspace Bomb. Two R.O.B.s activate it as the Minister flies away. Mario rushes towards the bomb in an attempt to deactivate it, but he is then knocked out of the stadium by Petey Piranha. Petey then locks the princesses in cages, and it is then up to Kirby to save them.
 Zelda/Peach Taken
Kirby defeats Petey and rescues Peach/Zelda. However, Wario jumps into the stadium wielding a Dark Cannon. After seeing a weakened Zelda/Peach out of the corner of his eye, he aims the cannon at her and fires, turning her into a trophy in the process. Wario nabs Zelda's/Peach's trophy and leaves, with Kirby and Peach/Zelda in hot pursuit. Kirby notices that the Subspace Bomb only has a few seconds left on it. As the stadium is consumed by Subspace, Kirby and princess escape in time thanks to a Warp Star.
 Pit's Descent
Pit sees the stadium engulfed by Subspace. Realizing the danger, Palutena approaches Pit and gives him the Sacred Bow. She sends him off to fight off the new threat to this world. Pit falls from Skyworld and begins to fly through the clouds.
 The Subspace Army In the Sea of Clouds
Pit lands somewhere in the Sea of Clouds. He then notices the Halberd, which once again drops off Primids. As they approach him, Pit splits the Sacred Bow into dual blades and prepares to fight them.
 Mario and Pit Meet
After defeating the Primids, Pit begins to survey the landscape. He notices Mario's trophy, which had been knocked there by Petey earlier. Pit revives Mario, who has a quick flashback to the events prior to his trophification. They then team up and continue to travel through the Sea of Clouds.
 The Arwing's Pursuit
After traveling for a while, Mario and Pit catch up to the Halberd. An Arwing flies past, and the pair turn around at the noise, and find that it's chasing down the Halberd.
 Kirby and Peach/Zelda Flee the Sea of Clouds
As Kirby and Peach/Zelda continue to fly through the sky on Kirby's Warp Star, the Halberd catches up to them and knocks them onto the ship.
 Arwing Downed, Peach/Zelda Overboard
The Arwing engages in a dogfight with the Halberd. While the Arwing dodges most of the shots, the Halberd's Combo Cannon Claw shoots towards the Arwing and knocks it out of the sky. The Arwing flies over Kirby and Peach/Zelda and from its wake comes a strong wind that blows the duo off the Halberd on its way down.
 Donkey Kong and Diddy Kong
Some of Bowser's minions are shown driving off in a Cargo with a huge hoard of bananas. Those who are left behind feel DK's wrath. Donkey Kong jumps out of the jungle and sees the troops driving off with the bananas. They fire three Bullet Bills at him from two cannons, only to have them shot down by Diddy and his Peanut Popgun. The minions flee the scene with the Kongs in pursuit.
 The Dark Cannon Aims for the Kongs
The Kongs find their banana hoard and beat their chests with delight. However, Bowser shows up and crashes the party. The Kongs prepare to fight, but Bowser pulls out a Dark Cannon. Not wanting to put Diddy Kong in any danger, Donkey Kong punches Diddy Kong out of the area and takes the Dark Cannon's hit, thus becoming a trophy.
 The Ancient Minister Escapes Mario and Pit
Mario and Pit catch up to the Ancient Minister, who is holding another Subspace Bomb. Mario jumps for it, but he can't reach. Pit jumps off of Mario's head to gain extra height, but he too can't reach it. The Minister escapes with the bomb still intact.
 Fox Confronts Rayquaza
Diddy is swinging through the jungle until he comes to a lake. Near the lake's shore, the Arwing that fought the Halberd earlier is crashed. Diddy goes over to investigate, but Rayquaza emerges from the lake. Seeing that Diddy has invaded its territory, it attacks the Arwing and captures him. It seems like the end for Diddy until Fox jumps from the burning Arwing. He uses Fox Illusion to set Diddy free. Rayquaza tries to hit Fox with another energy blast, but Fox sends it back with his Reflector. It hits Rayquaza and knocks it back into the lake. Fox gestures to Diddy, asking for his help to defeat Rayquaza.
 Diddy Kong Appeals to Fox
Fox and Diddy defeat Rayquaza, but when Fox tries to leave, Diddy pulls him back and tries to make him come with him. Fox ignores him and once again tries to leave, only for Diddy to drag him into the jungle by force.
 The Dissolving of the False King Bowser
Fox and Diddy defeat a False Bowser. Diddy touches it to make sure it's truly in trophy form, but it then dissolves into Shadow Bugs. Suddenly, a Dark Cannon shot shoots out of the jungle and just misses Fox and Diddy. The real Bowser is the culprit, and he shoots at them again. Diddy is willing to fight, but Fox knows that they're no match. He grabs Diddy and jumps off a cliff with him to safety.
 The Pig King Statue Targets Lucas
Lucas is seen walking very sadly through an abandoned zoo. Suddenly, Shadow Bugs drop from the sky and produce Primids. They surround Lucas, who shudders with fear. Then, the Pig King Statue appears and begins to chase down Lucas as he runs away through the zoo.
 Ness and Porky Face Off
The Pig King Statue continues to chase Lucas, until Lucas trips over a branch that is stuck in the ground. He tries to free himself, but fails to do so. Just when it seems like the statue will crush him, Ness shouts and targets a PK Thunder towards the Statue, which promptly knocks it to the ground. Ness then reveals himself on camera. The statue jumps up and prepares to fight, while Ness also jumps up and activates PK Flash. The attack shatters the statue and reveals Porky Minch himself underneath. Ness wipes the sweat off his forehead and prepares to fight while Lucas gets back up.
 Lucas Leaves Ness
Lucas catches up with Ness after they defeat Porky, only to find Wario looking down on them from a cliff. Wario laughs and aims the Dark Cannon at Ness. He fires, but Ness is able to dodge the shot. Wario fires several more times, but Ness dodges every shot. Realizing that Ness is a difficult target, he sets his sights on Lucas. He fires, but Ness pushes Lucas out of the way and takes the shot himself. Wario observes Ness' trophy while it rains, cackling madly. Lucas runs away, looking behind himself one more time as he does so. Lucas then bumps into the Pokémon Trainer some time later, who is about to take on a hoard of Primids. He summons Squirtle and prepares to fight them.
 Lucas Joins the Pokémon Trainer
After defeating the Primids, the Trainer calls back Squirtle and bids Lucas farewell. Lucas, however, is determined to save Ness, and he joins the Trainer on his journey.
 The Battlefield Fortress
An empty battlefield with a ruined castle in the background appears. Two R.O.B.s show up and prepare to detonate another Subspace Bomb. They hang their heads as the bomb explodes, engulfing them in Subspace. Marth sees all of this from atop the Battlefield Fortress, and he also sees a hoard of Primids approaching. Marth unsheathes the Falchion with a flash of light, and prepares to defend the fortress.
 The Meta Knight Encounter
Marth makes it to the patch of Subspace and stares at it. While he observes it, he notices a glimmer of light from the corner of his eye. Meta Knight charges in and attacks Marth, but Marth is able to block his attack. Meta Knight charges once more, and a fencing match then ensues. During the battle, Primids try to attack them, but Meta Knight and Marth are able to slice them in half. Realizing that they are on the same side, Meta Knight and Marth stand back-to-back and prepare to fight off the Primids.
 Ike Unleashes Aether
Meta Knight and Marth chase after the Ancient Minister, who is carrying another Subspace Bomb. Marth tries to slice it with Dolphin Slash, but he misses. Meta Knight flies towards it, but the Minister shoots his wings and forces him to drop back down. Suddenly, Ragnell is seen floating behind the Minister, and Ike jumps up and performs Aether to destroy the Subspace Bomb (oddly, he shouts "Great Aether!" instead of "Aether!"). As a result, the Minister is sent flying away. Ike then joins the other warriors on their journey. This is the only time in the entire story that the use of a Subspace Bomb is successfully prevented.
 Three Warriors and the Ancient Minister
Ike, Meta Knight, and Marth continue to chase the Minister, but the path ends at a cliff, and the Minister is able to escape.
 King Dedede Steals Peach/Zelda
A Waddle Dee is seen walking down a path. Upon seeing it, Luigi stands unsurely in a battle-ready pose, but the Waddle Dee just glances at him and walks away. Another Waddle Dee walks up and startles Luigi, prompting him to enter the same pose again. However, King Dedede walks up from behind him and strikes Luigi with his hammer, turning him into a trophy with one hit. Dedede dusts off his new trophy, and then prepares to ambush Wario as he drives up the road. As expected, Wario stops his Cargo and nabs Luigi's trophy. However, a huge army of Waddle Dees surrounds him and forces him to drop the trophy. Dedede reclaims it, and he proceeds to hijack Wario's Cargo with all of his trophies in tow. As Dedede and the Waddle Dees retreat, Wario jumps up and down in anger.
 Link Draws the Master Sword
 The Subspace Army In the Forest
As Link and his fairy continue to travel through the forest, Yoshi is seen sleeping on an empty stump. He wakes up for a second, but then goes back to sleep. Link then notices the Halberd as it drops off more Primids in the forest. Link prepares to fight them, and Yoshi wakes up to help Link.
 Link Loses the Battleship Halberd
Link and Yoshi pursue the Halberd, but they lose it when it flies too far away. Link notices another route and takes it with Yoshi right behind him.
 Snake's Cardboard Box
Snake's cardboard box is shown inside of the Halberd. Snake shakes the box a little from the inside.
 Zero Suit Samus Infiltrates
 The Pikachu Generator
Zero Suit Samus enters a room, ready to attack. The door closes behind her. Suddenly, she hears a noise, and sees a power generator with a Pikachu trapped inside. She notices that the Pikachu's electrical energy is being used by the generator, so she breaks it and rescues the Pokémon. An alarm goes off, prompting an army of R.O.B.s to come in. Samus and Pikachu get ready to fight them.
 Where is the Power Suit?
Zero Suit Samus and Pikachu enter a control room, and Zero Suit Samus notices her Power Suit on a computer monitor. It is locked away in a hidden room.
 Bowser's Surprise Attack on Zelda/Peach
In an area similar to those that Mario and Link are coming towards, Kirby notices something, then bolts in the opposite direction. Zelda/Peach calls out for him to stop, but Bowser appears behind her. Aiming his Dark Cannon at her and before she has a chance to react or move away from being shot, he fires. Her trophy hits the ground as Kirby runs in The background unaware of Peach/Zelda's Trophication and False Bowser storms up and disintegrates; the Shadow Bugs now move on to the princess' trophy.
 False Zelda/Peach Battles Mario/Link
Link/Mario and Yoshi/Pit are running along, and the camera switches to False Zelda/Peach, who (cumbersomely) pulls a Dark Cannon out and points it at the pair. Suddenly there is a slash, and the Dark Cannon is sliced in two; the False Princess falls back. Pit/Link is revealed, having sliced the cannon with his blade. False Zelda/Peach glares at him with hate. Pit/Link prepares to fight, and Mario/Yoshi runs up.
 Link's/Mario's Misunderstanding
Link/Mario stops running and sees Mario/Link and Pit/Yoshi having trophyized the False Zelda/Peach. While the trophy soon dissolves, a mislead and enraged Link/Mario attacks Mario/Link with his sword/fist, but Mario/Link dodges. Mario and Pit then face off against Link and Yoshi.
 King Dedede Nabs Defeated Link/Mario
Mario/Link and Pit/Yoshi defeat Link/Mario and Yoshi/Pit and turn them into trophies. Dedede drives by and Mario/Link sees Peach's/Zelda's trophy in the Cargo. Dedede delightedly nabs the trophied Link/Mario and Yoshi/Pit, but Kirby appears to Dedede's chagrin and slices the Cargo's arm, freeing them and reviving them. Link/Pit lands and shoots an arrow at Dedede as he escapes. The Cargo splutters, slowing down. The five heroes hurry in pursuit.
 The Cavern's Entrance
Mario, Pit, Kirby, Yoshi, and Link find the Cargo, now empty, beside the entrance to a cave.
 King Dedede's Castle Discovered
The five heroes discover King Dedede's castle. The clouds above are red and ominous, and the Halberd is silhouetted against them.
 Ganondorf Issues Bowser's Orders
Inside a ship, a large screen flashes and reveals Bowser. Bowser turns to face the camera, and a commander points to a point on the map: Dedede's castle. Bowser nods and trudges off, leading his small band of warriors; two Goombas, a Koopa Troopa and a Hammer Bro. The man is revealed as Ganondorf. He grins menacingly.
 Charizard Flies to the Ruins
Pokémon Trainer and Lucas stand on a cliff and watch a Charizard fly past. Recognising Charizard as one of the two Pokémon he is trying to catch, Pokémon Trainer prepares to catch the Pokémon.
 The Wario and Lucas Rematch
While walking towards the Ruins, Lucas and Pokémon Trainer are ambushed by Wario. Remembering what Wario did to Ness, Lucas clenches his fists and prepares to fight Wario alongside Pokémon Trainer.
 Wario's Trophification
Wario's trophy falls to the ground, defeated. Lucas and Pokémon Trainer stand over him, triumphant. Lucas then remembers Ness, and looks around, but is sad to see that there is no sign of him. Pokémon Trainer reassures him, gesturing that Ness may be inside the Ruins.
 King Dedede Pins a Badge on Peach/Zelda
Inside Dedede's castle, Dedede is examining his three trophies: Ness, Luigi, and Peach/Zelda. He brushes some dust off Ness and grins happily. Reaching inside his sleeve, he pulls out two Dedede Brooches, pinning them on Ness's chest and Luigi's nose. Coming to Peach/Zelda, he realises that he has none left. However, he notices his own, which he reluctantly pulls off and puts on her. Suddenly the roof gives way, and a huge chunk of stone breaks on Dedede's head, knocking him out. More stone rains down, and Bowser and his forces enter the throne room. As they look around, Bowser notices the half-buried princess. This is one of few cutscenes in the game to use a fade-to-black.
 King Dedede's Hidden Castle Passage
The doors to the throne room are thrown open, revealing the mess of stone. Mario, Link, Yoshi, Pit, and Kirby enter the room and see a crudely carved passage to the left of the throne.
 Bowser Kidnaps Peach/Zelda
Bowser is hurrying across a cliff with the captured princess in hand. However, Mario is hot in pursuit, bearing down for a punch. Bowser shields himself with Peach/Zelda, causing Mario to redirect his aim into the ground. Mario jumps back, and Pit fires an arrow at Bowser. The Koopa King dodges, but Peach's/Zelda's brooch flies off. Bowser stumbles and falls off the cliff, but he lands in his Koopa Klown Car, and flies off towards the waiting Halberd, laughing. Running past Link and Yoshi, Kirby looks at the brooch on the ground.
 Subspace Engulfs King Dedede's Castle
In front of the castle, the Ancient Minister watches two R.O.B's prepare a Subspace Bomb. The Ancient Minister flies off, leaving the bomb to detonate.
 Ganondorf Meets with Master Hand
In the same ship as before, the screen flashes and reveals Master Hand, who points at Ganondorf, seemingly ordering him to do something. Ganondorf nods and bows to Master Hand, but he secretly smiles evilly to himself.
 I Found You, Ivysaur!
Lucas and the Pokémon Trainer locate the Ivysaur trophy. The Pokémon Trainer tosses a Poké Ball and calls back Ivysaur.
 I Caught You, Charizard!
Charizard's trophy falls back, beaten. A Poké Ball flies through the air and captures Charizard. Pokémon Trainer looks at it with delight and Lucas looks up at him admiringly.
 The Hole in the Ruins
The Pokémon Trainer and Lucas walk through a corridor and find themsleves at the Ruined Hall and a dead end, looking around the large room curiously.
 The Tank in the Wastelands
Galleom is speeding through the desert in his tank form, with Ike, Meta Knight, and Marth watching from a distant cliff. Ike quickly jumps off the cliff to confront Galleom. The two remaining warriors rush forward after him, then look at each other. Meta Knight then jumps after Ike. Marth pauses, confused, but then jumps after the other two.
 Galleom Transformed
Ike, Meta Knight, and Marth catch up to Galleom, waiting for them in his tank form. He then transforms into his humanoid self, who then pounds his fists at them agressively. The three warriors raise their swords at Galleom, ready to fight.
 Three Warriors Defeat Galleom
Galleom, defeated, leaps off a cliff away from Ike, Meta Knight, and Marth. He lands on unstable ground at the front of the Ruins, near Wario's trophy. The ground gives way to Galleom, and he plummets into the unknown. The three warriors rush over to the cliffside, a large hole at the entrance to the ruins where Galleom fell.
 Galleom Tumbles into the Ruins
Meanwhile, the Pokémon Trainer and Lucas are still in the large room when suddenly, the ceiling gives way and Galleom lands in the Ruined Hall, knocking them back. Galleom gives them a menacing glare and pounds on the ground aggressively. The two companions prepare to battle the powerful robot.
 Galleom Self-Destructs
The duo defeats Galleom, and he snatches them up in one of his hands, rendering the Trainer unconscious. Galleom then activates a Subspace Bomb in its head and flies up into the sky. Lucas uses PK Thunder to sever Galleom's arm, making them fall as Galleom detonates in the sky. Lucas holds the Trainer to him, and right when they are about to hit the ground, Meta Knight swoops in and carries them away from the approaching void of Subspace, which sucks in Wario's trophy. Meta Knight flies the duo to Marth and Ike, where the trainer regains consciousness. Lucas offers his hand, and the Trainer shakes it.
 The Sorrow of the Ancient Minister
Yet another Subspace Bomb is being transported to its destination by the Ancient Minister, this time in a wasteland-like area. While he watches the patch of Subspace left behind by Galleom's detonation, he is reminded of the many R.O.B.s that have and will continue to be sacrificed. The Ancient Minister is brought out of his funk by one of Pit's arrows - the group of five has caught up to him again. He moves off as the group gives chase.
 The R.O.B. Army Rallies
The Ancient Minister shoots some lasers at Mario and Link, but they dodge every shot. After a few moments, the Ancient Minister drops the Subspace Bomb in place, crushing one R.O.B. Two other R.O.B.s prepare the bomb while others prevent Mario and Pit from disarming them. One R.O.B. waves to the Ancient Minister, who flies away in sorrow as the bomb explodes. Mario escapes by riding Yoshi, while Link and Pit hang onto Kirby's Warp Star.
 Falco Appears
Diddy and Fox are walking along a riverside path when Diddy is struck by a Dark Cannon without warning. Fox evades Bowser's next shot, but Diddy's trophy is quickly duplicated by waiting Shadow Bugs. Fox is in a pickle until Falco drops out of his Arwing, before destroying Bowser's Dark Cannon with multiple Blaster shots. Bowser leaves in disgust, but not before the False Diddy acculumates more Shadow Bugs and triples in size. Fox revives Diddy to a nasty shock as the three prepare to fight.
 Diddy Kong Appeals to Falco
With the Giant False Diddy defeated, Falco decides his work is done and starts walking away. Diddy attempts to recruit him just like he did with Fox, but Falco also refuses - he is quickly dragged away by Diddy, while Fox follows, bemused.
 The Floating Island of the Ancients
At long last, Diddy has found DK's trophy. However, he is on the Smash Skiff, and just as he is discovered, the Skiff flies towards a distance floating landmass - the Isle of Ancients. Diddy is noticably upset, but Falco calls in the Great Fox with a plan.
 The Copied Power Suit
Samus and Pikachu have reached the room where the Power Suit is being held. The two approach it, but two dark copies of it appear.
 Samus Revived
After the two False Samuses are defeated, an alarming amount of R.O.B.s enter the room. However, using her newly-recovered Power Suit, Samus destroys them all. She and Pikachu continue through the facility.
 The Destiny of Ridley & Samus
Samus and Pikachu now find themselves in a large circular room. Without warning, Ridley appears, grabbing Samus and scraping her against the wall. Pikachu quickly uses Thunder, which saves Samus in time for the real fight.
 Ruins on the Island of the Ancients
After defeating Ridley, Samus and Pikachu exit the facility. There are ruins similar to those found on the ground, but more noticable is a second building, this one with R.O.B.s actively carrying Subspace Bombs. The two prepare to enter.
 The Two Captains
Outside the Ruins, Olimar and a group of Pikmin are fighting against a giant R.O.B. While it seems to be going well, the giant R.O.B. wakes up and spins around, killing most of the attacking Pikmin. A red Pikmin taps on the quaking Olimar's shoulder and Olimar turns in time to see the Blue Falcon arrive. Captain Falcon attacks the R.O.B. with a vicious Falcon Punch. After defeating it he slides into a victory pose, accidentally killing almost all of the remaining Pikmin. Olimar and the aforementioned red Pikmin stare at him.
 Jump to the Smash Skiff
Captain Falcon and Olimar come to the edge of a cliff, where they see the Smash Skiff with DK's trophy. Falco and Diddy fly in to attack with Falco's Arwing. Falco opens the cockpit, dispatching Diddy, who activates his Rocketbarrels and opens fire on the skiff with his Peanut Popguns, blasting away the Primids stationed there. Captain Falcon, seeing this as an opportunity to fight, grabs a reluctant Olimar and jumps off the cliff onto the Skiff. Diddy Kong revives Donkey Kong, who breaks free of his chains and angrily beats his chest. Olimar and Captain Falcon complete their fall, and show themselves as friends to Diddy and Donkey Kong. More Primids hop aboard the skiff, and the Kongs and the Captains prepare to fight them.
 Donkey Kong's Rescue
Victorious over the Primids, Donkey and Diddy high five and dance around happily with Falcon and Olimar looking on. Falco then flies by in the Arwing and gives Diddy a thumbs up before flying away. Diddy waves after him before shade comes over the foursome. They see that the Skiff is entering the Isle of the Ancients.
 The Halberd Vs. the Great Fox
It appears that Falco has summoned the Great Fox as a distraction, as it is now in an all-out fight with the Halberd. Seeing this as an opportunity to reclaim his ship, Meta Knight starts climbing up a nearby mountain. On the way up, he passes by the Ice Climbers. Taking Meta Knight's quick pace as a challenge, the pair follow him up the mountain.
 Lucario Challenges Meta Knight
The Ice Climbers and Meta Knight reach the top of the mountain. On the very peak is a meditating Lucario, which quickly challenges Meta Knight to a duel. The Ice Climbers look on in worry.
 Meta Knight/Lucario Defeats Lucario/Meta Knight
Meta Knight/Lucario has won the duel, but quickly revives Lucario/Meta Knight.
 Meta Knight and Lucario Board the Halberd
With the duel over, the two combatants shake hands in respect. However, the Halberd breaks down through the clouds, ramming a trapped Great Fox into the mountain with great force. While the Ice Climbers fall down the mountain, Meta Knight and Lucario jump up to the Halberd.
 The Five Warriors
With the collision with the mountain, the Halberd dispenses a massive amount of Shadow Bugs. They fall to the base of the mountain, where Marth, Lucas, Ike, Pokémon Trainer, and the Ice Climbers are. While the group on the mountain's base prepares to fight, Mario, Yoshi, Link, Kirby, and Pit arrive to assist them.
 Snake's Mission Begins
Snake appears from his cardboard box onboard the Halberd.
 Lucario Discovers Snake
Hearing footsteps from behind, Snake quickly hides behind a pillar in a cardboard box. However, Lucario senses him with his aura and lifts the box, to Snake's shock. The three quickly team up to take on the approaching enemies.
 Princesses, Both Captured and False
Snake, Lucario, and Meta Knight arrive in a large room containing Peach and Zelda's trophies. Shadow Bugs quickly duplicate them both, so the trio prepares to fight.
 Snake Frees the Princesses
With the two False Princesses defeated for the last time, the trio rescues the real ones fom their cages. As they move off, Snake suggests that they remain where they are. The cutscene uses what is presumably a first-person-view shot from Snake's perspective.
 The Battleship Pleasure Cruise
As could be expected, the two princesses don't sit around. Sheik and Peach leave their room, ready to do some exploring of their own.
 Sheik and the Fallen Arwing
Sheik and Peach have reached the Halberd's deck, right next to the Combo Cannon. Fox chooses this moment to attack, causing various explosions near Peach. Thinking that Peach is Fox's target, Sheik leaps up to his Arwing and forcibly removes him from the cockpit. The two land on the deck and prepare to fight, but Peach stalls the battle by offering tea. Fox remains confused until he notices that Sheik is already drinking tea, and he accepts it.
 The Ones on the Bridge
Meta Knight, Snake, and Lucario have reached the Halberd's bridge. On it, various Mr. Game & Watches are at all the controls. Snake busts in and smashes them all out onto the deck below, causing them to melt first into Shadow Bugs, and then into Duon. Snake and Lucario jump down from the bridge while Falco drops in from his Arwing, joining up with Peach, Sheik, and Fox for the battle.
 The Conversion of Mr.Game & Watch
Duon is destroyed, its Shadow Bugs floating away. Mr. Game & Watch's trophy is revealed from underneath. Fox thinks it's hostile, but Peach revives him. Mr. Game & Watch wonders for a moment what happened to him before Peach tells him what happened. She also gives him her parasol to play with, which helped him join the group. Meta Knight then regains control of his ship.
 In the Subspace Bomb Factory
Samus and Pikachu are rushing through an industrial corridor with alarms blazing.
 The Melancholy of the Ancient Minister
With an explosion, Samus and Pikachu blast into the main storage room for Subspace Bombs. Dozens of R.O.B.s are there as well as the Ancient Minister. The pair prepare to attack, but the Ancient Minister's apparently depressed state give them pause.
 Ganondorf Takes Command
The group of DK, Diddy, Captain Falcon, and Olimar crash through the storage room's roof, landing right behind Samus and Pikachu. While they also do not attack, Ganondorf appears in holographic form. He gives the R.O.B.s new orders, but the Ancient Minister does not want to carry them out - he stops the confused R.O.B.s from grabbing multiple Subspace Bombs. With this, Ganondorf activates an override, causing the R.O.B.s to not only grab the bombs but to fire upon the Ancient Minister. He then sends in a flock of Auroros before ending the transmission. With the Ancient Minister's costume in flames, he casts it off to reveal that he himself is a R.O.B. and that he is in league with the other Smashers.
 The Countdown Will Not Stop
While Ganondorf's forces are repelled, the multitudes of Subspace Bombs are all set to explode. While some Smasher attempt to disable them, R.O.B. decide to have them all shut down, including himself. Captain Falcon remotely calls in the Falcon Flyer, so the Smashers—with DK carrying R.O.B.—escape.
 The Falcon Flyer
While falling down a shaft, the Falcon Flyer appears and the seven Smashers board it. But as the Flyer tries to escape the factory, Meta Ridley appears and starts chasing it down.
 Escape from the Island of the Ancients
With Meta Ridley destroyed, the Falcon Flyer manages to escape the Isle of Ancients before the entire island is consumed by Subspace.
 The Great Reunion
The Smashers at the base of the mountain look on as the massive patch of Subspace appears overtop the Isle of Ancients. As they watch, the Falcon Flyer and the Halberd both land nearby.
 The Great Invasion
A formidible ship emerges from the Subspace patch that is situated where the Isle of the Ancients once was. It fires its cannon, engulfing a distant area in Subspace. On the bridge, Ganondorf and Bowser watch the expansion of Subspace with grim satisfaction. Suddenly, they spot the Halberd closing in, and Ganondorf orders the secondary weapons to fire. Smaller cannons emerge from the Subspace Gunship's main cannon and unleash lasers on the Halberd. The Halberd puts up a short fight, but is soon destroyed by the cannons. From the wreckage, however, flies Samus' Hunter Gunship, an Arwing, Olimar's Hocotate Ship, and the Falcon Flyer. Ganondorf angrily calls for the smaller weapons to start firing as well. The four small ships bear down on the huge Subspace Gunship, but the turrets cannot land a hit on them; they are too small and their pilots are too good. Kirby flies in, riding the Dragoon. It slices clean through the Gunship, severing the main cannon and causing the entire monstrosity to be engulfed in explosions. Bowser and Ganondorf storm back into Subspace. The Arwing and the Flyer quickly follow, as Kirby flies along the disintergrating ship, followed by Samus' Gunship. The two of them also rush into Subspace, as the Hocotate Ship, spluttering and coughing, tries to keep up. As Olimar pilots his ship in, the Subspace Gunship is left behind to crumble into a flaming ruin.
 At the Entrance to Subspace
The heroes finally arrive in Subspace. They are all in a battle-ready pose patiently awaiting what is in store for them.
 The Crushing, Ruinous Defeat
The scene begins as Bowser and Ganondorf are shown walking through a portion of Subspace. Ganondorf decides to make his move and betrays Bowser by turning him into a trophy. He then goes to a cliff and summons Master Hand. He is attached by chains to an unknown figure who is revealed to be Tabuu, the ruler of Subspace. Ganondorf sees this and tries to attack Tabuu, who quickly defeats him and turns him into a trophy. Master Hand, enraged and free from Tabuu's wires, tries to hit Tabuu, who ends up defeating Master Hand just as fast as he did Ganondorf. All the heroes come rushing in after Master Hand falls. Tabuu then uses his Off Waves to turn every single character there into a trophy. Tabuu then combines all the colonies collected so far into one giant maze.
 King Dedede's Timed Badges
Back in Dedede's castle, now in Subspace, Ness, Luigi, and Dedede are all stuck in trophy form. Thanks to the Dedede Brooches, Ness and Luigi revive automatically. Ness realizes, from the look of the brooches, that Dedede must have saved them; he decides to awaken him. Once revived, Dedede gives them both a big hug, and they proceed to move through Subspace and rescue everyone else.
 King Dedede Vs. King Bowser
Dedede and his companions come upon Bowser. Dedede wanders over and revives the Koopa King. Bowser's eyes narrow and he leaps up and roars at Dedede, who raises his hammer to fight.
 The True Enemy Is Right There
Bowser falls back as a trophy. Once again, Dedede wanders over and revives him. Bowser's eyes narrow again, and he leaps up and roars again. Dedede smacks him on the nose and points at Master Hand. Bowser's shoulders slump as he reluctantly joins the good guys.
 Kirby Revived by Hunger
Kirby's trophy is lying by itself. Suddenly, he glows, and is revived. Hopping up, he spits out the Dedede Brooch and stares at it. A flashback shows him finding Zelda/Peach's brooch back at Dedede's castle. Looking around, he stares into Subspace, looking for someone else.
 King Dedede and Kirby Unite
Kirby discovers Ganondorf's trophy, but is shocked to see Bowser rush up and brutally beat up the trophy. Kicking it to one side, Bowser storms on, ignoring Kirby. Kirby is still stunned by Bowser's ferocity when King Dedede rushes up from behind and hugs him. Pointing towards the Great Maze, he wanders off, dragging little Kirby behind him.
 Link and Zelda Put Ganondorf to Action
Link and Zelda walk up to Ganondorf's trophy and, after a reassuring nod from Link, Zelda revives him. Ganondorf rises clutching at his head, and Link points at Master Hand's motionless form and the Great Maze. As the couple walk up the stairs, Ganondorf stares at his fist, wanting to destroy the pair, but knowing that he must first help to overthrow Tabuu.
 Wario Messes with King Dedede
Dedede is looking up at the Great Maze, when Wario tackles him from the side. Cheering and showing off, Wario poses and challenges Dedede, until he sees Ness and Luigi run and help Dedede up. Wario's jaw drops and the trio point in unison towards the Great Maze. Wario picks his nose and looks back, seeing the trio begin to ascend. Starting up his bike, Wario races up the stairs, satisfied that he beat them in some way.
 The Final Battle
Tabuu spreads his wings, preparing to use his Off Waves once again, when suddenly a bright blue ball shatters his left wing. As he roars in pain, the ball lands, skids around and shatters his right wing as well. The ball lands, spins and springs up, revealing Sonic, who waggles his finger at Tabuu. Tabuu shakes off his ruined wings and glares at Sonic with hate.
 The World Returns
Tabuu lets out a painful scream as he is defeated. Most of the places captured by Subspace turn back to normal, but the large amount of Subspace Bombs detonated at once have prevented the Isle of Ancients' reappearence. Then, all the characters appear, and look at the shining X where the Isle of Ancients used to be. After this, the credits roll.
 Toon Link Appears
 Jigglypuff Appears
 Wolf Appears
A Wolfen is shown flying to the stage Lylat Cruise. Then as the Wolfen flies over the ship, the camera takes the player to a view of the ships surface. Then, something obscures the view. It's Wolf, who makes a battle pose and let's out a grunt, which will then lead the player to a match against him.