There was once a world known as Mushroom World. There were 18 kingdoms that all existed in peace. However, one kingdom, known as the Koopa Kingdom, had a thirst for power and control. They began their plans long ago, but waited to enforce them. As this went on, two babies were being carried above by storks. They were delivering the babies to the Mushroom Kingdom by request of king toad. The koopas knew of this plan, and set up forts on a nearby island they thought was abandoned. King Koopa II allowed his son, Bowser, to control the towers while he stayed behind. As the storks traveled above, a koopa wizard known as Kamek attacked them and one of them was killed. The other crash landed with both babies on the island and were greeted by the Yoshis, dinosaurs that survived the ice age. The Yoshi's took the babies and nursed the stork back to health. They then infiltrated the forts and destroyed each of them. Bowser was severely injured on the island, and the koopas brought him back to the mainland. The stork then finished his flight to the mushroom kingdom, and told the king of the koopa's interference. The king declared war against the koopas, and they fought for over 20 years. However, peace returned when King Koopa II died during the battle. His son was the only heir left, but before he could do anything, a mystical being known only as Rosalina split the kingdoms in two, sending the Koopas into another dimension. The brothers later grew up, but they went separate ways. 

It had been 45 years since the defeat of the Koopas. Mario became a plumber, while Luigi became a cleaner. Mario was not satisfied with his plumbing job though, and longed to be a hero.  "Hey Mario!", said his employer, "I got another job for you!" "I'll be on it...", says Mario regretfully. He gathers his plumbing materials and drives off in his van. "Why can't I be a guard?", he asks aloud, "This job is not the greatest for me." He drives down the road and arrives at a green mushroom house. He knocks on the door, and goes to fix a toad's plumbing. "What's wrong?", asks the toad. "Oh, nothing.", says Mario, "I just am down today..." He finishes the job quickly, but he felt no satisfaction. He accepts the toad's payment, and then returns to his van. Suddenly, a large explosion is heard. "What was that?", he asks aloud. He looks around the corner and sees smoke coming from the castle. He gets in his van and heads for Peach's castle. He gets out and sees a large airship flying in the air. He heads inside the castle and heads up the stairs to the balcony. "Peach!!!?", he asks aloud, "Where are you?!" He sees a large creature heading for the airship holding peach in his hands. "You!", exclaims the creature, turning around. Mario looks up in shock. "Who are you?", he asks, "I am BOWSER!", exclaims the creature in a booming voice. He swings his tail, knocking Mario into the wall. "Be seeing you!", says Bowser, boarding the airship. Mario grabs onto the side of the airship as it flies away from the castle. Mario climbs onto the top of the airship and stands up to Bowser. "Put her down!", he exclaims. "You fool!", says Bowser, "I will get my revenge for what you did!" Bowser walks towards him, and grabs him by the waist. "Now get out of here!", he says. He swings around and throws Mario from the ship. Mario flies towards the ground and looks up, as the airship flies away. He hits the ground and everything goes black. 

"Mario you fool...", says an unknown voice. Mario lays in bed, having been picked up by someone. "Luigi?", Mario asks aloud. He sits up and comes face to face with his brother. "Why did you do it?", Luigi asks. "Do what?", asks Mario, "Try to save the princess?" "You shouldn't get involved in this war...", says Luigi, "This is not our fight." "But we can't just stand around and wait!", exclaims Mario angrily. "This war you've started has put a real toll on me!", says Luigi, "I had to leave my old mansion, because ghosts keep there!" "Well i'm going!", exclaims Mario. He prepares to leave Luigi's house, when suddenly the sound of engine exhaust is heard. Mario runs out the door, and Luigi follows him. A giant airship hovers above the village they are in, and suddenly, a green liquid is sprayed down. Mario shields himself, but feels no effects. However, toads nearby are covered in the liquid, and suddenly they mutate in large brown monsters. Mario then notices mushrooms on the ground mutating. He grabs one of them and puts it in his pocket. He then runs towards the airship, Luigi following regretfully, and jumps, landing on the deck of the ship. They then notice that koopas patrol the area. Mario jumps on one of them, knocking its shell off. He grabs the shell and throws it, knocking the other koopas off the side of the ship. Suddenly, a purple aura luminates around the ship and suddenly everything goes white. Mario stands up, propelled backwards from the shock and notices that the sky is dark. He runs to the edge of the deck, and backs up in shock. Pools of lava poured beneath them, large fortresses stand at the edges of the kingdom. Suddenly, a large explosion is heard. Mario looks over, and sees large bullets with faces crashing themselves into the sides of the ship. They crash land on the ground below, and try to hide, but armoured koopas surround them. The general walks up to them and faces Mario. "Welcome to Koopa Kingdom. We've been expecting you...", he says, grinning.

Mario looks around as he is led towards the castle. He sees multiple jail cells, all of which have been abandoned. The general leads him to a cell in the middle, and throws him inside. He then notices that Luigi is not there. "They must have taken him else where.", he says aloud. Suddenly, he hears the cries of a woman. "Mario!", says a voice, "Help me-" "Shut up!", says a deeper voice. "Peach...", says Mario aloud. He looks around for an secret exit, but there is none. He pulls out the mushroom he put in his pocket. It could be the only way out. He puts it in his mouth, and suddenly he feels great power within him. He grabs onto the cell bars, and pulls them off. "He has escaped!", exclaims a guard koopa. Mario runs down the hallway, but then he comes face to face with Bowser. "You!", he exclaims, "How did you escape?" He grabs Mario by the leg and brings him into the main castle hall. Peach stands in a cage in the corner. "Because of your interference, I cannot continue my original plans...", he says, looking at Peach. He throws Mario to the ground and sits down on his throne. "It's time you get what you deserve!", he says. He pulls a lever, causing a small koopa in a flying vehicle, with clown designs on it, to drop down. "Go, my son!", says Bowser, "Destroy this fool who dares to trespass on my kingdom!" Bowser Junior flies into the air in his 'clown car' and heads towards Mario. He pulls out multiple shells, and throws them down at him. Mario dodges the shells as they fall, and Bowser looks on approvingly. Mario jumps up, knocking bowser Junior to the ground. "It's not over yet!", screams Bowser Junior. He gets inside of his shell, and spins around Mario. Mario tries to dodge the attacks, and suddenly Bowser Junior stops. He stops to catch his breath, but suddenly Mario jumps on his head, knocking him out. "NO!", screams Bowser. He stands up and swings his tail, knocking Mario into the wall. "Must I do everything myself?", he screams aloud. He grabs Mario by the foot, and throws him into another wall. "You can't stop my plans!", says Bowser, "Soon, everyone of your precious citizens will be turned into my minions, and soon, the Koopa kingdom will return to its original dimension, where it will rule supreme!" "I won't let you do it!", screams Mario. Bowser laughs a deep booming laugh. "You are already too late!", he exclaims. Suddenly, a large mystical sound is heard. Mario looks out the window of the castle, and sees that they are inside a vortex. Bowser watches him, and laughs, knowing his plan has succeeded... 

Mario stands facing the castle window. The large castle had entered the wormhole, and was heading straight for the mushroom kingdom. "You have failed Mario.", says Bowser. "Not yet.", responds Mario. He jumps up, ready to attack bowser, but he is thrown backwards. Bowser walks up to Mario and grabs him by the neck. "Your time is over.", he exclaims. Mario struggles to break free, and Bowser throws him to the floor. "Say goodbye!", he exclaims. He boils up, his chest turning orange inside, and prepares to fire flames directly at Mario. Suddenly, before Mario can get burned, Luigi steps in front of him, having escaped the guards. He takes the full blast of the fire, and falls into Mario's arms. This was the final straw. Mario stands up, and grabs Bowser by the tail, throwing him into every wall. He then throws Bowser to the ground angrily. "You killed my brother!", he exclaims. Suddenly, the ground begins to crack. Mario steps backwards, as the ground falls beneath Bowser. He falls down towards the lava below and screams as he is encased in it. Suddenly, the castle crashes into a green hill across from the toad village. They had made it back to the mushroom kingdom. Mario grabs Peach and Luigi's body, and they head towards Peach's Castle. They lay Luigi's body on a table, and look at him solemnly. "I'm sorry.", says Peach sadly. Suddenly, a toad comes in carrying a green mutated mushroom. "What about this?", he asks. Mario grabs the mushroom and puts it in Luigi's mouth. An aura appears around him, and Luigi sits up. "I'm too old for this hero stuff.", he says, and they all laugh. They walk outside and look into the sunset smiling. 

7 test tubes sit in a broken up laboratory inside Bowser's castle. 7 mutated koopas step out of the tubes and look around. "Father?", they ask aloud. A figure shrouded in darkness comes in and looks at them. The figure laughs a loud booming laugh.

Somewhere in another laboratory in the castle, the general koopa, who was injured, is being nursed back to health on a medical table. He is injected with a blue formula, and suddenly he runs quickly around the lab. He looks at his shell, which is now blue, and smiles.