It is possible to take more than one path in the Subspace Emissary, so for the plot I will simply pick my own for the sake of clarity. However I will put in the other possible character in brackets. Also many of these facts are facts that came from the trophies, so, yeah.
Before the Smashers...
Let's just get this straight: there are two worlds. The World of Trophies, very much like Earth and the planet the Smashers(the characters) are on, and Subspace, the realm of darkness. Master Hand is the master of the WOT(let's call that for short) and the ruler of Subspace is a naked guy with butterfly wings - Tabuu. Tabuu wants to take pieces of the WOT and make them Subspace, so in preparation he made Master Hand to gather and arrange an army that will eventually make the Subspace Bombs - bombs that suck everything nearby into Subspace. In order to have Master Hand favor Tabuu, he made chains of light to control Master Hand. Later, he learns of Mr. Game and Watch, who has an infinite supply of Shadow Bugs. These Shadow Bugs are bugs that can turn into an entire Subspace Army - or False Smashers. Tabuu enslaves Mr. Game and Watch, and moves on to his next stage of preparation.
On the Isle of the Ancients, a floating island, is the home of a group of R.O.B. minions and a lot of technology. They all serve one master - the Master Robot. Tabuu's forces take over the island, and the citizens are blackmailed into becoming part of the Subspace Army. The R.O.B.s immediately begin designing the technology needed for the army, mostly the Subspace Bombs. The bombs need two lesser R.O.B. minions to detonate, therefore sacrificing themselves. They also make a gunship that can fire bombs with a simple button, but for it to penetrate into the WOT, they needed a massive collection of explosions, making it a portal. They have all the bombs ready, but there's one more thing... the dreaded Dark Cannons are invented, cannons that have an ability Tabuu has - the Off Waves - that can turn a Smasher into their "dead" form, as a trophy. There are few Dark Cannons, though, and were made to get rid of any Smashers that got in their way. Then, Tabuu had Master Hand find Smashers to join "his" operation and make the WOT "his". These are Ganondorf, Wario, and Bowser, along with other non-Smashers such as Ridley and Petey Piranha. Of course, neither of these characters are aware of Tabuu.
The final stage is to rule the Halberd, the ship of Meta Knight. The ship is the primary transportation for the army, and of course, Meta Knight tried to take the ship back, but failed. However, King Dedede, another Smasher, somehow manages to find out about Tabuu and his powerful Off Waves, and begins to worry that if every Smasher was turned into a trophy, then there would be nobody left to turn them back into their active form. (If one Smasher becomes a trophy, another Smasher can tap their trophy base and revive them). So Dedede made his special Dedede Brooches, whenever applied on a Smasher they will turn them back into their normal selves when the brooches activate. Tabuu, meanwhile, thinks that his preparations are complete, and proceeds to carry out his plan.
Note: several of these happen at the same time, but divided into separate articles to minimize confusion.
In the sky, in an arena called the Midair Stadium, there is a fight taking place. Two guest spectators: princesses by the names of Zelda and Peach, anxiously await the arrival of the two opponents. When they finally come, they come in trophy form but then somehow come to their selves: Mario, the fighter with overalls, and Kirby, the fungi who likes eating things. The brawl goes on, and the winner (either Mario/Kirby, depending on which character you picked, I'm going to go with Kirby as the winner) comes and inspects the trophy of Mario. Kirby thinks about it for a second, and taps Mario's trophy base. Mario wakes up ready to fight again, but then realizes that Kirby wasn't his enemy anymore, and much to the pleasure of the two princesses, they shake hands. Then, the Halberd appears, disposing millions of Shadow Bugs into the arena and forming the Primids, a major part of the Subspace Army. After Mario, Kirby, Peach and Zelda defeat the wave of Primids, a mysterious figure called the Ancient Minister comes in, and sets a Subspace Bomb that detonates in three minutes. Then, Petey Piranha comes, knocks out Mario with a cannonball, and has the two princesses in cages. Kirby comes and defeats the piranha, setting one of the cages free (let's say Zelda was saved instead of Peach). Wario suddenly comes out of nowhere, holding a Dark Cannon, and is about to shoot Kirby and Zelda before seeing the more helpless Peach, and shoots her instead. He takes her trophy, and runs off. Kirby and Zelda begins to pursue him but then Kirby sees the bomb detonating in five seconds... They give up Wario's chase and fly away on Kirby's Warp Star. Everyone else except for Wario, Zelda, Peach and Kirby are sucked into the bomb.
The entire time overhead in Skyworld, Pit, a young warrior angel, was watching both the match and the bombing. When he sees the bomb explode, the Skyworld goddess Palutena summons him and gives him the task of saving Skyworld and the world from the Subspace Army. Then she gives him a bow to use as a weapon. Pit descends into the clouds and shortly afterwards sees the Halberd approaching and dumping more Shadow Bugs. Pit begins his fight, where he shows that the bow could be taken apart to use as swords, and put together again. After fighting off the foes, Pit sees Mario's trophy where it had landed after Petey Piranha's punch. Pit revies Mario, and they team up to fight the remains of the primids and go after the Halberd. They weren't fast enough, but another ship, the Arwing, goes after the ship instead while the two continue their journey. In the meantime, Kirby and Zelda have traveled on the warp star to look for the Halberd themselves. Then the fog clears to reveal that they were about to smash into the ship, and crash on the roof of the Halberd. They weren't given enough time to explore the ship, because then the Arwing had the Halberd in combat. Being smaller, the Arwing is more able to dodge the shots but eventually got hit anyways, and when it crashed it nearly hit Kirby and Zelda. The gust was enough to make the two fall off the ship, eventually landing at Skyworld and after exploring the Sea of Clouds they make it to solid ground. Then they start looking for the Halberd on foot.
Then, somewhere in a jungle, very far away from Kirby, Zelda, Mario and Pit, Donkey Kong and his nephew Diddy Kong are trying to get their stolen bananas back. While they fight, pursuing the theives - Bowser and his Koopa Troopa minions - they meet Bowser himself with his Dark Cannon. He aims it at Diddy Kong and is charging when Donkey Kong comes up and punches Diddy out of the way and takes the shot himself. Diddy closed his eyes as the Dark Arrow strikes Donkey Kong.
Somewhere else, Mario and Pit are on solid ground, pursuing the Subspace Army. Then they come across the Ancient Minister and tries to get him, even with Pit jumping on Mario's head (it should be vice versa, and Pit could've used his wings) the minister still got away.
In the jungle, Diddy comes back to the area where there was a lake, and plans to look for help to save his uncle. Then he sees the wrecked Arwing from the Halberd pursuit, and Diddy investigates. However, the Pokemon (I know there's an accent) Rayquaza pops up and is obviously angry for people invading his personal territory. Rayquaza grabs Diddy, but then the pilot of the Arwing - Fox - comes and saves Diddy, and the two Smashers defeat Rayquaza. Fox is about to head off when Diddy stopped him, trying to get his help in order to find Donkey Kong. Fox walks away again and again, and eventually Diddy had to go and drag him by his collar. After traveling for a while, they see the Koopa King himself. Then they see his purple aura with yellowish eyes, but they defeat him anyways. After Diddy's short celebration the trophy melts, revealing the Shadow Bugs and the Bowser was a fake. Then the real one shows up, fires a Dark Arrow, but thanks to Fox they both jumped off a cliff (?!?!) and lived to tell the tale.
Now, the story comes to the Ruined Zoo, where you meet Lucas, a young boy. As he wanders around, he encounters some of the Subspace Army. Suddenly, his old enemy Porky Minch comes around, forcing Lucas to fight. After running away from Porky, Lucas's foot got stuck on a branch, and he cowered on the ground, waiting to die. Then, just as Porky was about to deliver the blow, there was a sudden cry of PK Thunder! and Ness, another EarthBound kid, descends gracefully. Porky explodes, revealing the spidery mechanic inside. After the two team up and defeat Porky, Wario appears and shoots Dark Arrows at Ness. Ness skillfully dodges them all, and Wario eventually moves on to Lucky Contestant Number Two: Lucas. Lucas stares at the gun in horror, and with a split second decision Ness comes and pushes Lucas out of the way. Lucas gasped as Ness's statue hit the ground, and runs away, leaving Wario with his new trophy.
Lucas continues walking around the zoo, and bumps into a tall Pokemon Trainer (I'm gonna call him PT). He spreads his arm aside, showing a large amount of Shadow Bugs. The two team up, and after defeating Porky they set off to a set of caves, where Pokemon Trainer plans to capture Charizard, another Pokemon.
Now, Marth, a prince from Fire Emblem, sees a bunch of Subspace minions emerging from a recently detonated bomb. The blue-haired guy holds out his sword and plans to attack thousands of them at once. After a long battle, he is at the edge of the detonated bomb. Suddenly, another blue guy races up to him and attacks with his sword, but then Marth reflected the blow and the two continues the blow. The new blue guy turned out not to be Ike, but Meta Knight, his sword Galaxia in hand. Both Marth and Meta Knight believed each other to be a member of the Subspace Army, but when Primids comes and attacks both of them, they realize that each other weren't the enemy and they team up to fight. When the primids are gone, they see the Ancient Minister, carrying yet another Subspace Bomb. They try to catch up to him, with Marth missing and Meta Knight forced to fly back due to the AM's laser beams. Suddenly, a third blue guy comes up, and using the Aether attack, cuts the bomb from the Minister, sending him somewhere far, far away. Ike - for of course it was him - joins the other two swordsman to form a trio and they proceed to pursue the minister in order to prevent him from setting off another bomb.
Now, King Dedede had learned that Bowser and Wario haad joined the Subspace Army and are turning Smashers into trophies for their personal collection. Thinking about his Brooches, he decides to start his own collection to save himself from Tabuu's Off Waves. He turns to find Mario's younger brother, a timid Luigi. After turning Luigi into a trophy with a hammer instead of a Dark Cannon, he sees Wario passing by on his Cargo. On the cargo were two statues: Ness and Peach (this could be Zelda if you released Peach from her cage first). Dedede's Waddle Dee minions leave the statue of Luigi by the road, and Wario, attempting to get his freebie, is ambushed by Waddle Dees. In the midst of the confusion, Dedede gets on the Cargo and drives away, leaving Wario there, jumping up and down and waving for Dedede to come back. No chance of that happening. Now Dedede has three trophies: Peach, Ness, and Luigi.
Now, in the Forest, Link from the Legend of Zelda comes wandering around and spies the Master Sword set in a tree trunk. He draws out the sword and shortly, after passing by the dinosaur Yoshi, sees the Halberd passing by, depositing yet another load of Shadow Bugs. More Primids emerge from the bugs, and Link and Yoshi decide to team up to attack the oncoming Subspace Army minions. Along the way, they try to pursue the Halberd.
Now, you are given the insider's view of the Halberd. Everything is neat and clean, except for a lone cardboard box sitting on a beam. It stirs, and the clip ends.
Finally, you meet Samus Aran from Metroid. Samus looks like a girl in her suit, but without her suit - Zero Suit Samus - she's just a plain girl with a blonde ponytail. She has infiltrated the floating island of the Isle of the Ancients, and is ready to sneak into the Research Facility to find out where her suit was. After defeating several R.O.B. goons, she sees the Pokemon Pikachu, who is apparently being tortured by a machine sucking his electricity to power the generator. ZSS uses her Plasma Whip to free Pikachu. As she does, the alarm sets off, so Samus and Pikachu team up to fight the goons. They arrive at a control center where Samus found a video screen showing one thing: her suit.
Kirby and Zelda, in the meantime, had found yet another lake after ditching in it after the Halberd thing. Kirby suddenly heard a noise and raced off to find it, leaving Zelda behind accidentally. Bowser suddenly comes by, holding a Dark Cannon, and blasts Zelda into the air. Behind Bowser emerges the clone, and it dissolves, snaking the way to Zelda's trophy. Then, right then and now, Link and Yoshi (or Mario and Pit if you rescued Peach, you'll see why later) are running their way to the lake, and False Zelda (the Shadow Bug clone) was holding the Cannon and trying to shoot Link. She never got the chance. Suddenly, Pit (or Link, if the princess is Peach) comes up and slices it in half. When Mario and Pit battle False Zelda and had her defeated, Link finally turns around to see Mario looking at a Zelda trophy, which of course is just a Shadow Bug clone. It dissolved, and Link believed that Mario had killed Zelda. Don't forget, Link and Zelda's association are the same to the way Mario and Peach are linked, apart from the fact that Zelda doesn't get captured by Ganondorf every other Saturday. Anyways, Link sees his lover being disintegrated, and charges up at Mario. Surprised, Mario and Pit brawled with Link and Yoshi, and eventually Link and Yoshi lost. Suddenly, Dedede appears, driving the Cargo, picks up the two trophies with the mechanical claw, and races off. Briefly, Mario glimpsed Peach, his lover. Suddenly, Kirby comes, for the noise he heard was the Cargo, and he instantly broke the claw, touches the base of Link and Yoshi's trophies, and jumps back. To Dedede's annoyance, he turned back, but the newly revived Link tries to shoot an arrow at the Cargo in thanks. He missed, but the five-man group - Kirby, Mario, Link, Pit, and Yoshi - set off the chase Dedede. They see the Halberd above Dedede's castle, and heads that way.
Ganondorf, another major member of the Subspace Army, knows that several trophies are in the castle below the Halberd. He transmitted the coordinates to Bowser, and now you realize that the Ancient Minister was not the leader of the Subspace Army (next to Tabuu) as people originally thought.
Now the story turns back to Lucas and Pokemon Trainer, chasing Charizard into a cave. Lucas and the trainer follows the Pokemon, who eventually led them to the surface and to the entrance to yet another cave. Suddenly they are confronted by Wario, whose appearance boldens up Lucas, as he remembered Ness. Squirtle - the trainer's Pokemon - and Lucas together defeats Wario, but when Lucas realizes that Ness wasn't with Wario - for of course he wasn't, because Dedede took it - he is distraught. Pokemon Trainer points to the next set of caves, and Lucas nodded, believing that Ness was in there.
King Dedede is back in his castle, with his three trophies. He decorates them with the golden Dedede Brooches, putting one on Peach's hands, Ness's chest, and Luigi's nose. When he gets to Zelda he realized that he only had three brooches, so he stupidly took the one he was wearing off, and gave it to Zelda. Suddenly, the ceiling exploded, revealing several Hammer Bros. and Koopa Troopas. Bowser was also there, ready to take his trophies. One piece of the ceiling hit Dedede on the head, turning him into a trophy. Bowser sees the trophy of Peach sticking out from the mess, and he takes it, completing the princess pair. He left the trophies of Ness and Luigi in the mess, completely unaware of their existence. Later, Mario, Link, Pit, Yoshi and Kirby arrive at the castle, catching up to Bowser and seeing the Koopa King escape. When Mario sees the sight of his enemy, he attempts to punch him, but Bowser blocks him with the new trophy. Pit fired an arrow which Bowser dodged - barely - but it forced the brooch off Peach and sent Bowser tumbling down a cliff. Luckily for Bowser, and unluckily for the Smashers, his Clown Car picks him up and it flies away to join the Halberd overhead. Kirby, ignoring his fellow Smashers' expressions about Bowser's getaway, investigates the dropped brooch. During that time, the Ancient Minister and his minions had deployed another bomb outside Dedede's castle, and Ganondorf watches it on a screen wherever he was. The detonation sucks in the castle, along with Dedede, Luigi, and Ness inside it. Then you get introduced to Master Hand. Ganondorf bows, but the glint in his eyes tells the truth: he had no respect for MH at all.
Now, back at the caves, Lucas and the trainer are still looking for their "treasures". Lucas was looking for Ness, while Pokemon Trainer was looking for Charizard. While they are there, they fight off more of the Subspace Army minions, and finds a trophy lying there. Not Ness, not Charizard, but another Pokemon - Ivysaur. After capturing Ivysaur they find themselves in a dead end, in an empty underground hall.
Meta Knight, Marth, and Ike had seen a major Subspace Army member Galleom patrolling the desert. They pursue it, first jumping off a cliff. Ike went first with no hesitation. Meta Knight and Marth looked at each other, shrugged, and Meta Knight hopped off. Marth scratched his head, as if to say, why do I have to hang out with these guys? and jumped off the cliff, too.
Galleom seemed to be very powerful, but with the three swords it was defeated. However, the monster jumped off another cliff (Marth didn't scratch his head this time), landing in the same place where Lucas and Pokemon Trainer are below. The ground couldn't take the weight, and G-force made Galleom fall. Lucas and Pokemon Trainer are astounded, but they get their wits back and defeat Galleom, again. When the health hits zero, Galleom unleashed his final card - a bomb inside him, detonating in fifteen seconds. Then he grabs the two boys, and launches himself up into the hole he had made. To Lucas's dismay, Pokemon Trainer had fainted, but remembering how Ness had sacrificed himself to save him, used his PK Thunder attack to sever the arm holding them. However, they fell, plunging to what seemed like death.
Not necessarily. Meta Knight, the only flyer of his group, raced in and caught the two boys before they crashed to the ground. The bomb detonated in the middle of the air, taking Galleom and the trophy of the defeated Wario with it.
Pokemon Trainer awakes shortly, crashed out on the ground. Lucas offers his hand, and with gratitude, the trainer took it. Lucas, Pokemon Trainer, Meta Knight, Ike, and Marth join teams happily.
Now, the Ancient Minister is in a different part of the desert, ready to detonate another bomb. However, he had witnessed the detonation of Galleom's bomb, oddly feeling sorrow for the sacrifices of his brethen every time they detonate a bomb. Before he could express his thoughts any further, Pit fires an arrow at him, catching him by surprise. The rest of the group arrives, and gives chase. The Minister does his best to avoid their attempts to stop him, firing shots the entire time. He drops the bomb, and the R.O.B. minions set it. No matter how hard the Smashers try, they could not be removed. One unit waves a good-bye to the Ancient Minister, who was still expressing his sorrow.
When the bomb detonates, Kirby, Pit and Link escape on a Warp Star, while Mario and Yoshi escape on Yoshi's back.
Now, Fox and Diddy Kong are traveling east throughout the jungle and the swamp, after jumping off the cliff. A Dark Arrow comes out of nowhere, to show Bowser standing with a Dark Cannon in hand. The Arrow hits Diddy Kong, turning him into a statue. Another swarm of Shadow Bugs form a False Diddy, leaving Fox alone. Bowser shoots more arrows at Fox, dodging them all skillfully, but both knows that he couldn't hold out forever. Then, an airship zooms overhead - another Arwing - and a figure jumps out of it. It turned out to be Falco Lombardi - Fox's wingmate. He kicks the cannon out of Bowser's hands, destroying it. Bowser fled in his Clown Car. (I'm not sure what happened here, because his old one got sliced in half by Pit, remember?) Anyways, Fox taps Diddy Kong's trophy base, whose false self had tripled in size during the diversion. Diddy freaks out at the sight of Giant Diddy, but eventually fights his false self. After defeating False Diddy, Falco heads off by himself, but Diddy drags him back, wanting his help for his search for Donkey Kong. Unfortunately, Falco headed off again, and Diddy was forced to drag him by the collar, like he did with Fox. Fox, in the meanwhile, had thrown his hands up in exasperation, saying exactly what Marth had seemed to say.
At a river ending in a waterfall, they see Donkey Kong's trophy on a Smash Skiff. Fox calls for his Great Fox, his and Falco's command vessel, and the three Smashers head off to save Donkey Kong.
Samus and Pikachu are still exploring the Research Facility, looking for the Power Suit. They finally reached it, but then they are confronted by two Dark Samuses, or False Samuses, or Shadow Bug Samuses, or Clone Samuses, or WHATEVER! Anyways, they brawl the two Samuses, and win. Suddenly, the alarm goes off (again), and more minions come in. However, as soon as they came in they are dispatched, as Power Suit Samus is back in action. Now they are searching for the command room to shut off the Research Facility. When they reach a dead-end, Samus encounters her arch-enemy Ridley, who grabbed her, taking her along for the ride. Her suit scrapes against the wall... and in an act of desperation Pikachu yells, "Pika!" and a thunderbolt rains down on Ridley. It lets go of Samus, who was very fazed but was still functional. The two defeat Ridley, and simply walk out of a secret door outside. Then, they see more minions holding more Subspace Bombs, and they follow them into what seemed like a bomb factory.
Now, outside on the Isle of the Ancients, sets a little astronaut named Captain Olimar. Olimar is engaged into commanding his minions, the Pikmin, to attack a very large ROB unit. The machine whirls his arms, wiping out most of the Pikmin. Suddenly, a very fast racing machine piloted by a super-fit bounty hunter Captain Falcon zooms in. Falcon destroys the unit with a single Falcon Punch (I wonder what happens when two Falcon Punches collide?) but unfortunately lands in an area where the last couple of Pikmin remain. Only one is left - the red one next to Olimar.
The two captains set off, and when they reach the edge of the isle, they see the Smash Skiff carrying Donkey Kong's trophy. The Great Fox comes in, dumps Diddy Kong onto the skiff, and ready to free his uncle at last. Smiling at Diddy and the Pikmin mishap aside, Falcon grabs Olimar and jumps off the isle.
Diddy Kong had just freed Donkey Kong when the two captains landed on the skiff. Suddenly, the see more Subspace Army minions, and after facing them off they see the skiff going into an insert area inside the isle. They find this as a perfect opportunity to infiltrate the place, and decided to go and strike the core of menace...
Meta Knight, Marth, Ike, Lucas and Pokemon Trainer are at the base of the Glacial Peak, where Meta Knight stares at his ship. He stares at it, and leaves his group behind, climbing the peak to regain control of his ship. As he does, he passes twin Smashers the Ice Climbers, and the two - Popo and Nana - take his climb as a race and races him to the top. The Ice Climbers eventually make it to the top with Popo and Nana reaching it seconds before Meta Knight. As they cheer, Meta Knight gives no care for them, his eyes looking at a strange, meditating, mystic Lucario, another Pokemon. He challenged Meta Knight to a duel, and the Ice Climbers just watch. (Here you can pick either Lucario or Meta Knight. I will pick Meta Knight.) When the blue Kirby won, he gave the trophy of Lucario some thought, and tapped the trophy base. The two shake hands as Kirby and Mario had done ages ago at the Midair Arena. Only this time, there weren't any Shadow Bugs coming after them.
Now, the Halberd. It is warring with the Great Fox, something that's not good. With a strike, the Great Fox lost, but the Halberd rammed it into the mountain, making everything crash. Meta Knight and Lucario move up to the ship, skillfully climbing the sides even in that tumult, while the Ice Climbers fall down the mountain, helpless.
Actually, not helpless. They met up with the remains of Meta Knight's group, although they're facing even more minions. However, Mario and his team walk right up, jump off another cliff (lots of cliff jumping today) and came to the rescue. After a very long fight, the two groups join up and are victorious.
Back at the Halberd, the cardboard box is finally seen again. This time, it shifts, and a figure emerges from it. Out comes Solid Snake from Metal Gear Solid, who was doing a Zero Suit Samus. He infiltrated the ship, and is sneaking through it when he senses Lucario and Meta Knight coming. Hiding himself in a box again, he thought he had gotten away, but Lucario's aura had allowed him to sense Snake in his box, and lifted the cover. Snake is thoroughly surprised, and the three - Meta Knight, Lucario, and Snake - are ready to fight until Lucario's aura allows him to sense more people coming - although people is a harsh word for it. Yes, more Subspace minions are on their way to attack, and the three quickly realize that each other weren't the enemy, and team up to fight the minions. After some exploration, they arrive at a room with two cages - each holding a princess statue.
More Shadow Bugs are snaking their way to the cages, each forming a False Princess. After battling False Zelda and Peach, reviving the statues, Snake tells the princesses to STAY PUT while he and the men look around.
Obviously, Zelda didn't listen. She transformed into her alternate disguise, Sheik, and the two make their own trip along the exterior of the Halberd, which is crazy in these wind conditions. But, they make it, and arrive at the front deck of the Halberd. At the same time they arrive in that area, Fox, now piloting yet another Arwing (how many does he have???) duels the Halberd again. (Third time, huh?) Sheik, thinking that Fox was shooting Peach, jumps up, and punches the glass of the Arwing. Fox ejected out of the Arwing, engaging Sheik to a duel in the middle of the deck. A violent duel is about to begin, and are even in battle position when they are stopped by Peach, holding out a cup of tea for Fox. Fox stares at her like she's crazy, and looks at Sheik, who was already sipping at her tea. Shaking his head in exasperation, he realized that the two weren't his enemy and accepted the tea.
Snake, Meta Knight, and Lucario have made it to the control room, where they see a lot of Mr. Game and Watch clones. They should be called Mr. Lame and Watch, though, no offense to anyone, for they were flying out through the window. Not much of a protector, huh? However, they melt into Shadow Bugs, forming the giant monster of Duon. Snake and Lucario jump out of the window, joining Peach, Sheik, and Fox, while Falco jumps out of another Arwing (OMG) and joins the fight. When Duon is defeated, and it melts into a trophy of Mr. Game and Watch, Peach revived him, gave him her umbrella, and let him join her group.
Meta Knight, in the meanwhile, had stayed behind to pilot the Halberd, for of course it was his ship. The Halberd has now been retaken.
Isle of the Ancients. While Pikachu and Samus are exploring the Subspace Bomb factory, Donkey Kong, Diddy Kong, Captain Falcon and Captain Olimar are planning their own infiltration of the bomb factory. The two groups cross paths in the final room... facing the Ancient Minister, more ROB minions, and hundreds of Subspace bombs. If one bomb can suck up a full castle like Dedede's or Marth's, then how much can hundreds deal? A lot. At first, it's only Pikachu and Samus, glaring at the minister (although how they could've known him is a mystery) like they hated him (which they did). Then, the minister hangs his head, showing remorse, apparently unwilling to set off any more bombs. Then, a hologram of Ganondorf appears right after the four other Smashers smash through the ceiling. The Ancient Minister stands in front of the minions, but Ganondorf had the enslaved minions attack their former master. Now the detonation can begin.
With the Ancient Minister's cloak on fire, he was now useless... or is he? Anyways, the Smashers attempt to attack the minions holding the bombs, but it was useless. Ganondorf vanishes in a flurry of Auroros, but not before the Ancient Minister blasts his green cloak apart... revealing his true self at last.
The Master Robot of the R.O.B.s and a Smasher. At last. Fully aware that these ROBs are the last of his brethren, his kind, he refuses to leave them. When Captain Falcon orders them to go, R.O.B. refused, and eventually he was tucked under one arm, carried throughout the way to the exit, with only a melancholy goodbye to the last of his kind.
As they jump on the Falcon Flyer, Ridley appears again, although he is now Meta Ridley, huge and powerful. It pursues the Falcon Flyer as they try to escape, forcing the Smashers to fight in mid-flight. After destroying Meta Ridley, they escape the island as the titanic explosion engulfs the island and more. Thanks to Tabuu and Ganondorf, ROB is the last of his kind.
In the desert, Mario, Link, Pit, Yoshi, Kirby, Marth, Ike, Lucas, Pokemon Trainer, and the Ice Climbers watch as the huge explosion happens off-shore. The Falcon Flyer containing Donkey Kong, ROB, Diddy Kong, Samus, Pikachu, Captain Falcon, and Olimar flies in and lands, right next to those who traveled by foot. Next comes Meta Knight, Peach, Zelda, Fox, Falco, Lucario, Mr. Game and Watch and Snake, arriving on the Halberd. Finally the Smashers meet up, planning what to do now.
The now completed Subspace Gunship emerges from the huge explosion, ready to fire. The bomb can suck bits of the WOT into Subspace with one hit. It shoots a shot to the side for a test shot, and is about to fire more when the Halberd comes up to the Gunship.
At once, the turrets of the Gunship begin to fire their shots at the same time. The Halberd, not as nimble as the Arwing or the other smaller ships. Although able to dodge some shots, the Halberd eventually takes a shot that pierces it cleanly. (Why does it have to be that the Halberd always sink in the ocean???) But as it explodes, smaller ships emerge from the wreck - the Falcon Flyer, Samus's gunship, Fox and Falco's Arwings, and Olimar's Hocotate rocket. They skillfully dodge every single shot fired at them, and as they do it, Kirby, flying solo on his Dragoon, emerges from the side, and pierces the Gunship cleanly. It begins to disintegrate, and Ganondorf and Bowser, standing at the top deck, angrily heads back into Subspace.
The ships nimbly move into the massive portal, which wasn't hard considering its size, and enter Subspace at last.
Once there, all the Smashers - Mario, Peach, Donkey Kong, Diddy Kong, Yoshi, Link, Zelda, Samus, Pit, Ice Climbers, ROB, Kirby, Meta Knight, Captain Olimar, Fox, Falco, Falcon, Pikachu, Pokemon Trainer, Lucario, Marth, Ike, Lucas, Mr. Game and Watch, and Snake - finally begin their search for the true terror at hand.
Ganondorf and Bowser are ready to report to Master Hand, but then, Ganondorf realized that he didn't need to listen to the hand anymore, and ready to usurp the position. Using his Dark Cannon, Ganondorf shoots Bowser, casually kicks his statue aside, and walks up to the Hand. Now that he looks at him in person, he realized the binding chains of light tying his fingers. With shock and horror, he looks up and meets Tabuu for the first time. He realized that he was being used, and attempts to attack him, but with only so much as a wave Tabuu turned him into a trophy. Rendering him powerless, the trophy spirals back, but the force was enough to cut the golden chains of light binding Master Hand. Curling itself into a fist, it launches itself at Tabuu, but is shunt back. The Smashers then arrive at the worst possible moment, which Tabuu used as a chance to use his Off Waves and turn everyone into trophies. Everyone was rendered powerless, and they scattered everywhere, and at last the taken parts from the WOT circled Tabuu, who finally had no obstacle any more.
In the place of the Subspace Realm where King Dedede's castle is, the brooches finally work. With some bright light, Ness and Luigi are awakened, and both stare at each other in amazement. They both stare at the brooches, looked up at Dedede, and understood. With gratitude, they freed Dedede, who heartily clapped them on the back, fully knowing that Tabuu had set his Off Waves, and they should go and free all the other Smashers. They do so, collecting every statue they can see, reviving them. When Dedede, Luigi and Ness arrive at the place where Master Hand lies, they see the trophy of Bowser. Dedede leaps forwards and revives him, and with anger Bowser faced Dedede off in a match. When he is defeated, DDD revived him AGAIN, and when Bowser attempts to thwart the king again Dedede casually smacks him across the mouth, pointing to the rest of the scene. Looking at the remains of Master Hand and Tabuu, Bowser understands and grudgingly joins the team.
Meanwhile, more bright light is coming from the trophy of... Kirby! Gasping, the pink fluffball spat out something gold - a Dedede Brooch. Remembering it seemed like a long time ago, when Kirby had swallowed the brooch when it had fallen off Peach (or Zelda)'s arm. Realizing what happened, Kirby sets off for his own exploration of Subspace, ready to fight.
When Kirby reaches the area Dedede is, both had completed their journey and when they meet, Dedede gives the famous Dedede glomp, hugging him tightly. Then, without further ado, Kirby is dragged by the arm, by none other than the King Dedede, doing a Diddy Kong.
In the meanwhile, Bowser is venting his anger at Ganondorf for turning him into a trophy. Bowser is chewing, kicking and punching at the trophy of Ganondorf, but eventually joins Dedede, Ness, and Luigi up the stairs... to Tabuu, to the spheres of the WOT surrounding him, forming a big maze. The Great Maze.
If you revived Wario during Kirby's run, Wario will come and thwart Dedede, groaning about the stolen Cargo car. However, when he saw Ness and Luigi - two of the trophies he had - were on Dedede's side, he reluctantly understood about Tabuu and joined their team.
Similarly, if Link and Zelda were revived during both runs, they would go up to Ganondorf's trophy, Zelda would nod, and they would revive him. Ganondorf wakes, but Link and Zelda walk ahead, towards Tabuu. Ganondorf considers attacking them with a Dark Arrow, but decides against it, reluctantly following them to Tabuu.
The bad guys become good guys. Bowser, Ganondorf, Wario and King Dedede used to be villains, but are now good. The only obstacle is... the Great Maze.
The Great Maze is basically all the levels rolled into one - while looking for the False copies of the Smashers. After defeating each one, you can face Tabuu. Just as Tabuu is about to do the Off Wave ability again, something flashes through him, and out of nowhere...
You've probably been wondering, where did Sonic go? Yes, the speedy hedgehog attacked Tabuu, crippling his wings and his Off Waves. Sonic joins your team, and attacks Tabuu.
If Tabuu is defeated, all the explosions unexplode, aside from the Isle of the Ancients, which could not be replaced due to the massive damage. However, Tabuu is defeated, and the heroic Smashers escape Subspace and back into their own world.
The Smashers stand on a cliff face and share a brilliant sunset. The Brawl Main Theme plays, finally allowing you to see the lyrics, and Tabuu is finally defeated.
Whatever that had happened to Wario's Dark Cannon is unknown.
