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See SmashWiki's article on The Subspace Emissary for more information and the complete plot.

The Subspace Emissary is the Adventure mode in Super Smash Bros. Brawl.[name reference needed] It tells the story of the Subspace Army, led by the Ancient Minister, and its attempt to bring the world into Subspace. The story includes every playable character featured in the game except Toon Link, Jigglypuff, and Wolf who can be found on certain levels after beating the story. Most levels appear to require the player to choose between one of a few characters that are available. There is also a Co-op mode that allows two players to play at the same time. Most of the enemies in the Subspace Army make their debut in Super Smash Bros. Brawl, while most of the bosses have appeared in previous Nintendo titles.

Link, Zelda, and Ganondorf in the Subspace Emissary

Zelda, Peach, Mario, and Kirby ready to fight the Primids at the Midair Stadium

Princess Zelda is one of the first characters introduced in the Subspace Emissary. She, along with Princess Peach, watches a friendly match between Mario and Kirby in the Midair Stadium. However, the Halberd appears soon after, and Zelda and Peach rush to the stage when the stadium begins to get invaded by the Primid. When the Ancient Minister appears and drops a Subspace bomb, Mario is blasted away by a cannonball when he tries to stop it. Zelda and Peach are then captured by Petey Piranha. It is at this point that Kirby can choose to save either Peach or Zelda by destroying one of their Cages.

Link retrieves the Master Sword from its pedestal

After Kirby saves Peach/Zelda, Wario, a member of the Subspace army, appears and points the Dark Cannon at Kirby and the rescued princess but then notices that the other princess is in a more helpless position, choosing to shoot at her instead. This causes for the helpless princess to be instantly turned into a trophy, which Wario grabs before fleeing the stadium. Although Kirby and Peach/Zelda try to go after him, Kirby notices that the Subspace Bomb will detonate in 5 seconds and grabs the rescued princess, allowing the pair to escape the explosion by riding on a Warp Star. They continue to fly through the sky on Kirby's Warp Stay until the Halberd appears behind them and causes them to crash-land on the battleship's roof. Eventually, an Arwing begins to engage in combat with the Halberd, but the ship's Cannon Claw eventually hits the Arwing. As the Arwing is on its way down, it manages to knock Kirby and Peach/Zelda out of the Halberd and into the ground below. Once there, Kirby hears something off in the distance and runs in its direction, leaving Peach/Zelda behind. Bowser then appears and immediately shoots the Dark Cannon at the princess, turning her into a trophy. This allows Shadow Bugs to take over it and make a clone of the princess while Bowser retreats with the original trophy.

Meanwhile, Link, accompanied by a fairy, is walking through a forest and reaches the resting place of the Master Sword. With both hands, the young hero retrieves the sacred blade from its pedestal and continues to walk through the forest, walking right by a napping Yoshi. Soon after, the Halberd is then seeing flying over the scene, dropping Shadow Bugs which quickly into Primids. Yoshi wakes up and helps Link successfully fight off the foes, and although the pair loses the Halberd as it flies far off into the distance, they continue with their pursuit.

If Peach was saved

If Zelda was saved

Master Hand giving orders to Ganondorf

Back at the control room, Master Hand gives Ganondorf the orders to destroy the Isle of the Ancients, and although the Evil King bows obediently, he secretly smiles malevolently to himself. Meanwhile, Link and the rest of the group find the Ancient Minister in a desert and pursue him, trying to stop him from detonating another subspace. Mario and Link begin to approach the Minister while dodging the lasers he fires at them. Despite their best efforts, the Subspace Bomb still explodes while the heroes barely escape the blast.

Sheik fights against Fox

Later on in the story, Snake, Lucario, and Meta Knight find both Peach and Zelda's trophies stuck inside cages in a room aboard the Halberd. However, Shadow Bugs swarm over the trophies and create clones of both princesses. Once 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 they leave, Zelda transforms into Sheik (to hide from Snake, for him not to know the princesses went out) and she, along with Peach, makes her way through the exterior of the Halberd despite Snake's order. Eventually, they make it to the front deck of the Halberd while Fox, once again in an Arwing, engages the Halberd and destroys one of the airship's turrets, shooting near where Peach was walking. Thinking that Fox was aiming at Peach, Sheik teleports onto Fox's Arwing and, using her hand, shatters the cockpit window. This forces Fox to eject out of the Arwing and land on the battleship's front deck along with Sheik. Although the two begin to fight, Peach stops them by offering a cup of tea to Fox. Fox, confused at first, looks over to see that Sheik has already begun drinking the tea, thus realizing that Sheik and Peach are not his enemies as he accepts Peach's offer.

Ganondorf orders the R.O.B. Squad to detonate all of the Subspace Bombs

Once Meta Knight, Lucario, and Snake make their way to the Halberd's main control room, they realize it has been taken over by various copies of Mr. Game & Watch, which they send flying through the window. The clones land in the front deck where Zelda and the rest of the group were, causing the clones' Shadow Bugs to turn into Duon; however, Zelda and the rest of the group successfully defeat the Subspace foe, and Meta Knight reclaims his ship. Back at the Island of Ancients, Samus Aran, Pikachu, Donkey Kong, Diddy Kong, Captain Falcon, and Captain Olimar infiltrate the Subspace Bomb Factory and come upon a room where they meet the Ancient Minister in a room full of Subspace Bombs, backed up with remnants of the R.O.B. Squad. Although the Ancient Minister looks entirely unwilling to perform any more detonations, Ganondorf then appears as a hologram and orders the R.O.B. Squad to activate all the Subspace Bombs. When the Ancient Minister gets in their path, Ganondorf presses an override button that forces the R.O.B.s to ignore the Minister, setting his cloak aflame with the R.O.B.s' lasers. Before disappearing, Ganondorf sends a flock of Auroros to distract them as they helplessly try to stop the Subspace Bombs. Suddenly, the burning Ancient Minister fires beams from his eyes, destroying the Auroros, and reveals that he, himself, is a R.O.B. who was disguised, and proceeds to help the others fight the advancing Subspace troops.

Ganondorf confronts Tabuu

After the Isle of the Ancients is engulfed in Subspace, Ganondorf appears on the Subspace Gunship as its commander along with Bowser, but he retreats into Subspace with Bowser when the Gunship is destroyed by Kirby and his Dragoon. Link and Zelda, along with another 10 smashers, enter the Subspace and begin to explore the area. Meanwhile, Ganondorf and Bowser are on the way to report to Master Hand, but he decides it is time to usurp Master Hand's position and aims at Bowser using the last remaining Dark Cannon, turning him into a trophy. Ganondorf kicks the Bowser trophy out of the way and goes up to a ledge, bowing before the Master Hand, who was actually a puppet of Tabuu, the supreme leader of the Subspace Army. Although Ganondorf tries to attack Tabuu, he is defeated and turned into a trophy. Soon after, Link, Zelda and the rest of the Smashers arrive to see the defeated Master Hand and look up to see Tabuu, but before they are able to do anything, the Master of Subspace unleashes his powerful Off Waves attack, turning every smasher into a trophy.

Ganondorf, Zelda, and Link getting ready to head into the Great Maze

Eventually, King Dedede's brooches revive Luigi and Ness. The duo then revive King Dedede and go out to revive the other characters. Later, 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 that King Dedede's group did not come across along the way. When Kirby finds Ganondorf's trophy, the resurrected Bowser appears and brutally attacks his trophy as an act of revenge (for being shot by his Dark Cannon) before tossing it aside. If Link and Zelda were rescued during Kirby and King Dedede's exploration of Subspace, a cutscene will show them both agreeing to revive Ganondorf, at which point they show him where their common target is: Tabuu inside the Great Maze. Together, Link, Zelda, and Ganondorf help the other Smashers throughout the rest of the story, eventually defeating Tabuu.

Toon Link's Role

Toon Link has a minor role in the Subspace Emissary and only appears if the player enters a secret door in The Forest after clearing the Subspace Emissary.