Fast-Food Chain From Another Dimension is the story mode for Crystal Warriors. It plays like a standard SSE-esque umbrella story.
Long ago, the god of Happiness, Pharrell Williams, was creating a formula for unlimited happiness. However, one faithful day an army of Reptillian Space Ninjas, led by Michael Bay, god of EXTREEEEEME, assaulted Pharrell's castle and stole most of the formula. (Scraps of it have been recovered and used in Pharrell's first solo hit song many years later. The song was simply titled "Happy.")
One day, in Michael Bay's lair, one of the space ninjas stupidly spilled the unfinished formula onto an empty Happy Meal box, creating a distorted abomination. The distorted abomination, also naming itself "Happy," killed most of the Space Turtles and stripped Michael Bay of his godly powers, before going into a deep coma for many years...
Soon after his defeat, Michael Bay became a film director. Not long after the release of his latest movie, one starring four of his remaining Space Turtles in colorful bandanas, "Happy" had awoken again...
...and this time, he's coming for us.
The story starts as Mario, Luigi, and Rosalina are chasing Bowser in his Koopa Clown Car. It appears that Bowser has kidnapped the princess, and Luigi, having enough of Mario being the big shot, tries to save Peach by himself. However, a portal opens, and Burger Monsters come out of the portal. Mario and Rosalina fight off the Burger Monsters, while Luigi, Bowser, and Peach are teleported away in a beam of dark burger magic. After seeing traces of the burger magic, Mario and Rosalina try to follow it to it's source.
After the level is beaten, it shows a cutscene of Raymond talking to a mysterious voice. The voice says that an old foe has risen once again, and tells Raymond to look for the one person who can stop him. The voice then shows a hologram of a pink haired girl with a red ribbon in her hair wielding a magical bow. Raymond nods his head and sets off.
Raymond is exploring Mitakihara in search of finding Madoka, when suddenly a building gets destroyed, revealing an army of Transformers. It is revealed that Michael Bay brainwashed the Transformers to star in a movie series directed by him, but after discovering the critical backlash of the newest installment of the franchise, "Transformers: Age of Extinction," Bay flipped out and used the Transformers to kill anyone in his way to regain his godly power. Raymond tries fighting the Transformers, but is soon assisted by Mami Tomoe. After defeating the Transformers, Mami agrees to help Raymond find Madoka, and the two begin their search, fighting off Burger Monsters along the way.
McDonalds Labaratory Part 1
Luigi wakes up and finds himself in a dark labaratory, where he meets up with Sayaka Miki. Luigi and Sayaka then come across an army of mutated Koopa Troopas with hamburger buns for shells. After defeating the mutants, the two come across Bowser. Luigi suspects Bowser is the one behind it all, and attacks him. However, after defeating Bowser, they discover that he is innocent. Bowser and Luigi reluctantly join forces when Happy appears and tries to trap them all in a Happy Meal box, when a lance like weapon hits Happy, stopping him. The wielder of the lance is revealed to be Kyoko Sakura, who orders the others to charge at Happy, but Happy teleports away just in the nick of time. Kyoko, Luigi, Bowser, and Sayaka then defeat the remaining burger soldiers and escape the Lab.
Finn and Jake are playing a video game at the Treehouse when suddenly the house is attacked by a robotic replica of Ronald McDonald. After the battle, the Ronald-Bot kidnaps Finn and leaves Jake to fend for himself. Jake fights off many burger creatures before escaping the Treehouse, meeting up with Mami Tomoe and Raymond.
Happy Meal Factory
In the heart of the Labaratory, which is a small factory that produces Happy Meals and other McDonalds products, Mario, Rosalina, Finn, Ruby Rose, Weiss Schnee, and Madoka Kaname are trapped in a cage hanging over a pit of lava. Happy appears and says that he plans to gather the greatest heroes in the multiverse and turn them into burger meat for his evil Burger Monster army. However, using a strange combination of Finn's sword attacks and Madoka's magic abilities, the six break out of the cage and face off against Happy. After defeating Happy, it is revealed to be a replica. The six then decide to try and find an exit to the factory.
At Stark Tower, Nick Fury and Iron Man are investigating the nature of the Burger Magic. They have a small sample of Dark Burger Energy, but the energy soon flips out and possesses Iron Man's suit. Nick Fury then sends out a signal, and Data, Mika Sho, Alpha, and Link bust through the room. After defeating the possessed suit, Iron Man joins the team. Nick Fury sends the five to the McDonalds Labaratory, to see who is behind Happy's attacks.
Asterob is training for an upcoming tournament at ;Lavendera, when he is confronted by Rockoon. Asterob and Rockoon briefly quarrel, before an army of Transformers attacks, prompting Rockoon to flee. Asterob tries fending off the Transformers, when Jake, Mami, and Raymond come to his assistance. They fight the leader of the Transformers, a mind-controlled Optimus Prime. After the battle, Raymond frees Optimus, and the team carries on.
McDonalds Labaratory Part 2
Luigi and his team search through the Labaratory, and decides to split up. Sayaka and Bowser go in one direction, while Luigi and Kyoko go in the other.
Luigi and Kyoko find Peach and Francesca trapped in cages, guarded by the Death Egg Robot, which Happy has taken control of. A third cage bursts open, revealing Rocket Raccoon, who helps the duo defeat the robot. The team then frees Peach and Francesca from the cages.
Meanwhile, Sayaka and Bowser make their way to the exit. After escaping the Labaratory, they are picked up by Iron Man's team on the Helicarrier.
Yang and Blake are on a mission in the Forbidden Forest when they are confronted by an army of Grimm Creatures, supposedly led by Cinder. Yang and Blake fight against the Creatures, and then prepare to fight Cinder. A mysterious ninja going by the name of Sheik appears and defeats Cinder, and decides to help Yang and Blake. Raymond, Jake, Mami, Optimus Prime, and Asterob soon show up, and Raymond uses a teleporting device to warp them to the McDonalds Labaratory, to stop Happy once and for all.
McDonalds Labaratory Part 3
Mario, Rosalina, Finn, Ruby, Weiss, and Madoka escape the factory and fight off Badniks along the way. Raymond's team warps in using the Teleporting Device. Raymond says that he needs to speak to Madoka, and the two warp out of the Labaratory for a bit, to discuss the matter at hand. The remaining Crystal Warriors are then pit against a huge army of Burger Creatures. The team defeats most of them but Happy appears and traps the team in a cell.
A little while later, Raymond and Madoka teleport back in only to be completely seperated from the group. The two search for the team throughout the Lab but ends up finding Luigi's team instead. Raymond and Francesca reunite, and the team is sent through a portal.....
Raymond, Madoka, Luigi, Kyoko, Francesca, Peach, Rocket, Sayaka, Bowser, Data, Mika Sho, Link, Iron Man, and Alpha all end up in a realm of darkness that was formed by the mere existence of Happy, titled "Voidspace." They fight off an army of Waddle Dees led by a possessed Kirby. The team defeats them and frees Kirby, only to be confronted by Michael Bay. Michael Bay claims that he was granted dark powers in exchange for loyalty to Happy and his master. He uses magic to knock Madoka unconscious, so that she doesn't get in the way, and he sends the Ninja Turtles to defeat Raymond and his friends. After defeating the Ninja Turtles and Michael Bay himself, the heroes journey on through Voidspace in hopes of finally defeating Happy, as well as his master.
While unconscious, Madoka has visions of a black haired girl fighting against a small feline creature.
Burger Kingdom Part 1
Mario, Rosalina, Finn, Ruby, Weiss, Yang, Blake, Sheik, Jake, Mami, Optimus Prime, and Asterob are all trapped in a cell, soon to be used as pawns for Happy's plan. However, a metal saw-like blade bursts the cage open, and Mega Man appears to help break them out. The Crystal Warriors escape, and end up in a dystopian Burger city. They find out that while they were captives, Happy and his army took complete control over the Mushroom Kingdom, Hyrule, Mitakihara, The Candy Kingdom, and other locations, and added them into his kingdom. Mario and the others fight back at the soldiers, aided by fellow rebels Marceline and Maka Albarn. Knowing that they are hopelessly outnumbered and outmatched, the Warriors retreat into a small cave.
The Cave Of Hope
The Crystal Warriors enter what is dubbed "The Cave of Hope," where The Minecrafter is mining ores to be used as weapons. She reveals that she gathered many other rebels to help retake all the kingdoms and slay Happy. Among the rebellion army are heroes such as Miita Knight, Whyti & SaturnDiva, Marine the Raccoon, Kamina, Hiccup, and Knuckles. The Minecrafter provides the Warriors with the materials she has so far, and continues to mine. A few hours later, a small army of burger-fied zombies, skeletons, and creepers attacks the group, but they are soon defeated. Now, all eqquiped with diamond armor and swords, Mario and The Minecrafter lead the team into battle against the Burger Army.
Heart of Voidspace
Raymond and his team enter the Heart of Voidspace, where they spy on a conversation between Michael Bay and a small white cat-like creature with red eyes. The creature accuses Bay of failing him, and transforms him into an eldritch monster with wings, an octopus-like head, swords for fingers, and spikes all over his body. After a difficult battle, Raymond and his team defeat Eldritch Bay, thus re-awakening Madoka. However, Madoka has gone insane during her time comatose, and attacks the team. She escapes through a portal into the real world, which is slowly becoming a part of Voidspace. Raymond tries to follow her, but Happy stops them, and sends his last minion to defeat them: Ridley. Raymond and his team defeats Ridley, and chases after Happy throughout Voidspace.
Burger Kingdom Part 2
As Voidspace and The Real World slowly begin to merge into one, the diamond-clad rebels charge at the Voidspace army, causing them to retreat. However, Madoka begins to attack them, having been mutated by Happy. Mario and the rebels defeat the mutated Madoka, returning her to her normal state. Mami discovers that there is a small place where the realms of Voidspace and The Real World overlap, and that they can enter Voidspace through the Overlap. Mario and the others get ready to face Happy, and charge into the overlap, with their weapons ready.
The Rebels enter The Overlap, and see that it is growing rapidly. Mutated burger creatures start attacking them, commanded by Happy and a mutated Raymond. On the other side of the Overlap, The Rebels see the rest of Raymond's team trying to fight back against the mutants. Mario faces off against Raymond, as the rest of the rebels fight back against Happy's army. Raymond is turned back to normal by Mario as the two of them, as well as a small group of others (Mika Sho, Finn, Alpha, Ruby, Madoka) face off against Happy. Meanwhile, Mami and The Minecrafter notice that almost the entirety of The Real World has been Overlapped. The mutants chase The Rebels into the small part of The Real World that remains.
Pocket of Reality
The rebels are cornered, as mutants surround them at every angle, and Happy uses his energy to make The Overlap grow even quicker then before. Mario and the others fight against Happy once and for all, but Happy's energy begins to overload, causing him to become an entity that even the god Pharrell can't match. Madoka, Mami, Sayaka, and Kyoko try to use their magical powers to make the team more powerful in hopes of evening the odds, but Happy easily is able to fight back, damaging Madoka and almost knocking out the other three magical girls. Francesca and Marine try to distract him as Mario deals some deadly blows with his fire powers. Soon the team outmatches Happy, but he has one more trick up his sleeve. He sends out a dark copy of Pharrell Williams to fight against the heroes to buy Happy some time to recharge. However, while Mario and the others are fighting the Pharrell Double, Mami, Sayaka, and Kyoko all attack Happy at once, leaving him with little energy left.
Mario and the others defeat the Pharrell Double, and the entire team charges out against Happy, and he is defeated by the heroes after a long and grueling battle. The mutated creatures dissolve into darkness, and the overlap shrinks until Voidspace is detatched entirely from existence, becoming it's own realm where shadows wander aimlessly. The rebels become world-wide heroes, and they go to Angel Island to celebrate.
In a post-credits scene, it shows a shrivelled Happy talking to the cat creature. The cat creature deems Happy unworthy, and transforms him back into his original form: a McDonalds Happy Meal. A tiny mutant nibbles on the chicken nuggets included in the Happy Meal, before shrivelling up into a mere shadow like the others did.