One day, at Bowser’s castle, Iggy walks in with some bad news.
Iggy: Hey Dad, Mario and Luigi have broken through our defenses and are headed here! Princess Peach’s forces have us surrounded on one side, and the Bros. are on the other side!
Bowser: Get all remaining forces to regroup here!
Iggy: Uh, the only ones left are already inside the castle, and the Mario Bros. are picking them off as we speak.
Bowser: You get out there and help! Where are your siblings?
Iggy: They have been defeated by the Mario Bros. already. The only reason I'm here is because he attacked my castle first, which gave me plenty of time to recuperate and come here.
Bowser: Get Kamek to come here immediately.
Iggy: Yes, Dad.
Iggy walks out the door. A few minutes later, Kamek walks in.
Kamek: Yes, your Gnarliness?
Bowser: We're surrounded! Do you have any ideas what to do?
Kamek: I've got one. The Bros. are too hard to fight, but Peach’s forces aren't, even with our small handful of survivors.
Bowser: Ok. Get them to do that.
Kamek radios the Koopa Troop to turn around and fight Peach’s forces. This diminishes the Koopa Troop even further, leaving only 100 soldiers left, but Bowser and his men are able to escape.
Kamek: Where to now, my Liege?
Bowser: I know a place…
At a safehouse in the Beanbean Kingdom...
Kamek: Ok, so we get a squadron to attack here, and here, and that's when we get the evac.
Bowser: Good, good. Just one question.
Bowser: THAT'S A PICTURE OF THE BEANBEAN CASTLE. I DON'T WANT THEM ATTACKING US, TOO.
Kamek: You have nothing to worry about. We've had a new recruit to the Koopa Troop. With this attack, we shall be a force to be reckoned with...
In Peache’s war room...
Toadsworth: Ok, so intel has shown that they are in a safehouse somewhere in the Beanbean Kingdom.
Toad General: What do you suggest we do?
Toadsworth: Before we apprehend them, we must put a stop to an attack they are planning on the Beanbeans’ castle.
Toad General: How?
Toadsworth: Luigi has signed up for the attack in his Mr. L suit, and will put a stop to it.
Toad General: Ok.
Above the Beanbean castle, in a doomship...
Troop Officer: Ok, so you are to rappel down with these 7 Fire Bros, and cause mayhem. You will be picked up at the entrance of the castle.
Luigi: When do I start?
Troop Officer: We're arriving right now. Go, rope down.
Luigi grabs a rope and rappels down to the entrance of the castle.
Troop Sergeant: Johnson and Green Guy, on me. You 4, take a left.
Soldier: On it.
Troop Sergeant: Bob-ombs, out!
The unit throws Bob-ombs everywhere, destroying the dining room.
Troop Sergeant: Move up! Fire, out!
The unit sprays their fire everywhere, burning down the throne room.
Johnson: We got hostiles, coming up the rear!
Troop Sergeant: Use any remaining weapons!
The unit carves a path to the exit and makes a run for it.
Troop Sergeant: Team 2, we are leaving, now!
Soldier: Roger that, we're coming.
Troop Sergeant: There’s the doomship! Johnson, take him out!
Johnson points a freeze ray at Luigi.
Luigi: What are you doing?!
Johnson: Just following orders.
Johnson freezes Luigi and gets onto the doomship with the rest of the squad.
Just then, Queen Bean, Lady Lima, and Prince Peasley run out of the destroyed castle, to find a frozen Luigi.
Queen Bean: This was the work of the Mushroom Kingdom. I will not let this stand. Have him sent to the dungeon. Tomorrow, we will launch a strike on the Mushroom kingdom.
At the Safehouse...
Kamek: Sir, I've been informed the attack went off without a hitch.
Bowser: Good. This should weaken their defenses, as they've weakened mine.
Kamek: What shall our next move be?
Bowser: We will wait. Let the Beanbean kingdom and the Mushroom Kingdom take each other out. Then we strike.
In Toad Town...
Bean General: ATTTTAAAAACCCCCCKKKKKKKK!!!
Hundreds of Bean soldiers attack the town.
Toad 1: Ahhh!!!
Toad 2: What do we do!
General Bean: Face your game overs like the true cowards you are!
Bean General: ATTAAAAAAAAACCCCCCKKK!!!
Don: The gig’s up! Let's get outta here!
In Peach’s castle...
Toadsworth: The attack has been ruined. They think that attack was supplied by our government! Why didn't we just give them a warning?
Toad General: What do we do now?
Toadsworth: We find Bowser, and capture him. Mario, Luigi is gone, it's all up to you. You must first help weaken the Bean population. I'll try to contact their queen.
Toadsworth: (on phone) Hello, Queen?
Queen Bean: Yes?
Toadsworth: Why are you attacking us? I thought we had a 1,000-year-old treaty?
Queen Bean: I did too! Then you just go ahead and attack our castle? There were innocent civilians, people of royalty, brave soldiers in there, you know?
Toadsworth: We didn't do it! It was Bowser!
Queen Bean: Then why did I find Luigi at the scene?
Toadsworth: Uh, er, well...
Queen Bean: Goodbye!
Toadsworth: Oh dear! They're the victims in the eyes of the world. No one’s going to say a thing while they destroy our kingdom.
At the border...
Toad Officer: Mario! It's good you're here, I was beginning to lose hope. We need you to break their line of defense so we can charge. Now move!
Mario goes to the border and shoots fireballs everywhere, then throws Bob-ombs at them. He eats a Mega Mushroom and stomps them out.
The Beans fall back.
The Toads charge, pushing the Beans all the way back to Hoohoo Village.
Toad Officer: Ok, good job! Just flank around our men, and you can go find Bowser!
Mario goes around the battle and finds himself in a forest. He makes it rhough, and goes to Beanbean Castle Town. Peasley confronts him.
Peasley: Hey, how dare you show your face around here, after what your kingdom did?!
Mario: We didn't do anything.
Peasley: You're lying, we know you did, we captured your brother in front of the castle.
Mario: Yes, but he was going to stop them, but they ambushed him and froze him. And now brave soldiers are getting game overs for the work of Bowser; it was his attack and those were his men.
Peasley: Why didn't he stop them before the attack?
Mario: I don't know! Just get your men to stop fighting and I'll get ours.
Peasley: No! I want an answer. Why didn't Luigi follow orders and stop the attack BEFORE it happened?
Mario: I DON'T KNOW, I'M NOT HIM, OK? If you have him in captivity, why don't you just interrogate him?
Peasley: He still hasn't thawed. Now come here!
Peasley pulls out a sword and swings at Mario. Mario dodges and throws a fireball at him, which Peasley easily parries. Peasley grabs Mario and swings, but Mario grabs his sword and throws it away, then knocks him to the ground with a punch.
Mario: Where is he? Now!
Peasley: I'll reset before I tell you.
Mario pulls out his hammer and beats his face in, leaving him badly injured.
Mario: Tell me, NOW!
Peasley: Ok, stop! He's in the pipe section of what remains of the castle, just let me go!
Mario throws him to the ground and pulls out his Mailbox SP.
Mario: (typing) I've just got an update on Luigi's location, he's in the Beanbean castle, I got this.
He rushes off to the Beanbean castle.
In the Beanbean castle...
Luigi regains consciousness in a room. His hands are tied, and he is in a chair. He has electrodes taped to various parts of his body.
Bean Guard: Why did you do it? We had a peace treaty!
Luigi: I didn't do it! It was Bowser! I'm telling you what you want to know!
Bean Guard: Why were you at the crime scene then?
Luigi: Because, they froze me with a Freeze Gun!
Bean Guard: You’re lying. Do you know what I do with liars?
30 volts are sent through Luigi's body.
Luigi: Ow how how how! Why? I'm telling you the truth!
30 volts are sent through Luigi's body.
Luigi: Errrggghhh... Please... stop...
Bean Guard: Then tell me the truth.
Luigi: I AM!
30 volts are sent through his body.
Luigi: *breathes hard* Ugh... huh... Bowser. My mission was to capture... Bowser. We almost had him. Almost. Errgghh...
Mario: Hee ya!
Mario hammers the Bean guard and unties Luigi.
Luigi: Thanks. Let's get outta here.
Mario: Come on.
Mario helps Luigi walk out.
Mario: Now, where to?
Luigi: Because I was talking so much about Bowser, the Beanbean government gathered intel on Bowser, but they don't know his exact location. It is somewhere here.
Luigi points to the Woohoo Hooniversity.
Mario: Let’s go.
The duo travel to the Hooniversity, which has turned into a military camp, guarded by the Koopa Troop.
Mario: We have to keep this quiet. Let’s go.
They both sneak in through a window and stealthily make it to the door leading to Bowser’s room.
Luigi: We need a key!
They see an officer strolling by, and jump him. They search for a key, get one, and unlock the door. Inside are Bowser and Kamek.
Bowser: Whaddya want?
Bowser turns to see Mario and Luigi.
Bowser: You two? How did...
Mario: It's all over!
They walk in, locking the door behind them.
Kamek flies out a window.
Bowser: I'm going to finish you off, once and for all!
Bowser breathes fire but the Bros. jump out of the way. Mario throws his hammer at bowser, Luigi following suit. Bowser covers his face in pain as he staggers around the room. Luigi trips him, and Mario grabs his hammer and deals a stunning blow to his head.
Mario: It's over, it's done.
Luigi: Not yet. We have to gather evidence that Bowser attacked the castle, instead of us.
Mario and Luigi look around the room. The amount of evidence in the room is staggering.
Mario: Oh yeah. Grab anything you can!
They grab evidence and leave as stealthily as they came in. They return to Beanbean Castle Town, awaken Peasley, and show him the evidence.
Peasley: This... This is... Bowser. He did it. All along. Him. I didn't believe you. But it was him.
Mario: Call off your forces, and it will be even!
Peasley: Done. You do the same, and we will capture Bowser.
Peasley pulls out his flying pillow.
Peasley: Hop on!
The trio fly above the battlegrounds where the war is being fought.
Peasley: Everyone stop! We have come to an agreement! Stop, immediately!
Mario: Mushroom army, you must also stop! We have located the true mind behind the attack, he is at Woohoo Hooniversity! Stop fighting and go there immediately!
Both armies march together in harmony to the Woohoo Hooniversity. They easily wipe out what little remains of the Koopa army, and find Bowser and Kamek, who returned to tend to Bowser.
Toad Officer: We know you are in there! Come out with your hands on your heads and your weapons on the ground. We will spare you if you follow orders.
Bowser and Kamek walk out, and Kamek puts his wand on the ground. 2 guards chain them up and put them in a doomship, to be shipped out to a big prison.
Outside of Princess Peach’s castle, Queen Bean walks up to a stand with a microphone and begins a speech. Mario, Luigi, Peach, Toadsworth, Peasley, and Lady Lima are all sitting in seats on either side of the stand. In front of the stand there are thousands of people, from both kingdoms, who have come to listen.
Queen Bean: The Beanbean Kingdom has suffered many tragedies through its history, including Cackletta having attacked it, and then Bowletta; and now Bowser, this evil being, has attacked our humble kingdom's castle, so that his sick humor could be satisfied watching brave soldiers give their lives fighting. For nothing. Two kingdoms, confused, fighting each other. The Beanbean Kingdom would like to extend its apologies for the ended games suffered by the Mushroom Kingdom. Innocent civilians. Brave soldiers. For nothing...
Queen Bean walks away, silently weeping, and the audience applauds. Princess Peach walks up to the stand.
Princess Peach: I understand how angry the Beanbean Kingdom's queen would be. They lost a castle. Not just a castle: a testament to the inspiration of the Beanish people; a monument to the kingdom’s history. Gone. Forever. We should have focused more on saving it than on being heroes and arresting Bowser. Now, thousands of soldiers are gone forever, due to our lack of responsibility. But the queen is beating herself up. It is Bowser who is at fault. He started this war, not her. He will remained imprisoned, for the remainder of his life.
She walks away silently, and hugs the queen. The audience cheers and applauds.
At the Prison...
Bowser: Well this stinks...
Bowser: You said that the plan would work.
Kamek: I never said that!
Bowser: So you thought it wouldn't work?
Kamek: I never said that either. I'm going to bed.
Bowser: I'M GONNA END YOUR GAME!!!
Bowser chases Kamek around the cell until 2 guards inject them with tranquil.
Bowser: I'm... Uhhhh... ZZZZZZZZZZZZZZZZZ *snore* ZZZZZZZZ
Guard: Big dummy.
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