The story begins on a rainy day in Dark Land. Bowser Jr. is walking down the hallway in pain after being bruised by Roy, when he slips over Lemmy’s ball. Lemmy comes in.
Lemmy: Hey Vincent! Leave my ball alone, you dope!
The same thing happens with all the other Koopalings, excluding Karma, because she’s on her monthly attack on Mario. Jr. goes to his room and starts to cry. He looks at his picture of him and Bowser, which has written on it:
To my favorite Koopaling
Love,
King Dad
Bowser Jr: I’ve had enough of this! I’m running away tonight!
That night at 3:00 in the morning Jr. packs his paintbrush, his wand, his picture of himself and Bowser, and some food and water. He then leaves Dark Land, with it still raining. He runs away to Pipe Land to make his new home.
The next morning…
Bowser: Jr. get up, breakfast!
All the Koopalings, including Karma, now back from her attack, are eating their pancakes.
Bowser: Jr! Get down here now.
5 minutes pass and Bowser goes to Jr’s room, only to come back in tears.
Clawdia: What’s wrong, hon?
Bowser: Jr. ran away!
Bowser starts sobbing as well as does Clawdia.
Roy: Big deal!
Meanwhile Bowser Jr. puts on a Mushroom disguise and renames himself Todd Landry. He goes to Toad Town and meets Wario and Waluigi.
Bowser Jr. (in disguise): Hey you!
Wario: Hey Waluigi! Look what have here! A Mushroomer.
Waluigi: Ha ha! Kid, what do you want with us?
Jr: Quiet! I need to talk to you privately.
Jr, Wario, and Waluigi go in an alley
Jr: I am Bowser Jr, Bowser’s son. Don’t tell anybody! I want to hang out with you guys.
Wario: Ok! But first of all, I’m not in it for you. I’m in for the money. You understand?
Bowser Jr: Yes.
Waluigi: Hey guys, I found something! It’s a map to a pyramid in Desert Land. It leads to a lost city of gold.
Wario is already on his way to Desert Land. Jr. takes of his disguise.
Waluigi: Hey! Put this cloak on to disguise yourself.
Jr: Ok.
He puts on his cloak and follows Waluigi to the Desert Land pipe.
Meanwhile in Castle Koopa…
Koopatrol: We can’t find him, King Bowser!
Bowser: Then he’s not dead. Double your search!
Koopatrol: Yes sir, we’ll look all over Plit for him.
Bowser walks over to a nearby Kamek
Bowser: Kamek, go tell the Koopalings to return to their castles in their lands.
Kamek: It will be done, King Bowser.
Kamek leaves to inform the Koopalings of Bowser’s message.
Meanwhile, back in Desert Land. Waluigi and Bowser Jr. have caught up with Wario.
Waluigi: Wario! Be patient. The pyramid is just ahead. Then you can have all the money you need.
Wario is daydreaming about all that gold.
Bowser Jr: I have a feeling I shouldn’t have come.
Wario: Why is that, bandana boy?
Bowser Jr: Morton’s here along with a search party.
Waluigi: SEARCH PARTY?! Wario! I told you we had a bounty on our head.
Bowser Jr: Waluigi, you’ll be fine. It’s not you guys they’re after. They’re after me.
Wario: All because you ran away!
Bowser Jr: Come on already, let’s get that gold.
Wario, Waluigi, and Jr.. enter the pyramid.
Waluigi: It’s dark in here, and there are mummies.
Wario: Hey, it’s a pyramid, what do you expect?
They make it to a pit. However, that pit is filled with very hungry Piranha Plants.
Wario: This ought to be fun.
Wario is about to walk down when Jr. uses his paintbrush to make a bridge to the other side.
Bowser Jr: Hurry.
The three cross the bridge only to find a two-headed dragon guarding the entrance to the city of gold.
Wario: This isn’t going to be easy.
Bowser Jr: Attack him! It’s the only way we can get past here.
Waluigi: He isn’t gonna get us.
Bowser Jr. jumps on the dragon and sprays paint up its nose. This causes the dragon to sneeze slime all over the area. Wario and Waluigi grab hold of the tail. Wario bites it, causing it to run around the room. Jr. falls off in the process. Waluigi climbs up the dragon’s back and hits it with his tennis racket and baseball bat. The dragon shrieks in pain before getting stabbed in the stomach, its weak point. The dragon runs around the room and crashes into a wall and dies.
Wario: Now that it’s dead, we can get my gold.
The three enter the next room to find it full of gold and jewels.
Wario: At last, the lost city of gold is mine! But how do I get this out of here and into my castle?
Bowser Jr: I’ll use my wand to warp us and the gold and jewels back to your castle.
Waluigi: Yes! This is ours.
Jr. gets out his wand and teleports Wario, Waluigi, himself, and the gold and jewels to Wario’s castle
At Wario’s castle…
Wario: Oh, this money will only make my castle look better.
Waluigi: Ah, the gold!
Bowser Jr: My first adventure with you guys turned out great!
Wario: This is great! Now I can make the Eiffel Tower out gold.
Waluigi: We can make statues of ourselves out of gold.
Bowser Jr: Great idea!
For two weeks the three would come across treasures while Bowser sent out more and more minions to find Jr. Princess Peach soon realized this and called for a meeting in her castle. That day Mario, Luigi, Yoshi, Toad, Wario, Waluigi, and a disguised Jr. were at the castle for a meeting.
Peach: I have arranged a meeting because Bowser has sent out extremely high numbers of troops all over Plit.
Mario: They’re not attacking anybody. They’re looking for something or someone. They might just be looking for a war.
Peach: Mario, I do not want another war. We’ve been over this, Mario.
Yoshi: But with so many troops out, the guard on Bowser’s castle will be thin.
Mario: I will launch an attack on Bowser’s castle. It shouldn’t be too hard. I’ll bring Luigi with me in case there’s trouble.
Wario: Hey, we want to go too!
Waluigi: Yeah! We want to help.
Peach: It’s settled then. The Mario Bros. and Wario Bros. and their little friend will go to Bowser’s castle. Let’s move.
Later in Dark Land…
Mario: Follow my lead.
Wario, Waluigi, Jr, and Luigi follow Mario to Bowser’s castle. With them is an army of Yoshis. Inside the castle, Kamek is rushing to Bowser.
Kamek: Bowser! The Mario Bros. and Wario Bros. and someone else are here.
Bowser: Oh no! I sent so much of my army to search for Jr. that my guard here is too thin. Send what troops we have and attack.
Kamek leaves to get the troops ready. About 300 Goombas and Koopa Troopas are launched.
Bowser: We’re terribly outnumbered. Tell Captain Hammy to prepare my doomship for takeoff.
Goomba: Yes sir.
The Mario Bros. and Wario Bros. see Bowser.
Bowser: Mario! I knew you were behind this attack. Now go away.
Mario: I’ll deal with this, you guys get on the doomship.
Luigi, Jr, Wario, and Waluigi get on the doomship.
Mario: Bowser! Why are you sending all your troops out of Dark Land?
Bowser: That’s none of your business.
Mario grabs a Fire Flower and shoots fireballs at Bowser. Bowser gets a stick and tries to hit Mario with it but Mario gets a stick of his own, and they try to hit each other with the sticks until they break. Bowser runs and gets on the doomship. Mario grabs on to a pipe connecting to the doomship. It leaves Bowser’s castle even though Yoshis try to hit the ship. Mario gets on the roof and falls through, meeting up with Jr, Wario, Waluigi and Luigi.
Waluigi: What happened?
Mario: Bowser escaped as usual. You hide in the storage room while I sneak through the airvent.
Everyone except Mario goes into the storage room. Mario is in the control room vent. He is listening to Bowser.
Bowser: Have you found Bowser Jr?
Hammer Bro: No sir.
Mario falls out and gets noticed by Bowser.
Bowser: Mario! So you stowed away, eh?
Mario: I’m not the only one you’ve got.
Two Koopatrols come in with Jr, Wario, Waluigi and Luigi.
Bowser: Well if it isn’t Fat Boy and his sidekicks Skin ‘N Bones and Mr. Green How nice of you to stop by. And who is this?
Bowser takes the disguise off, revealing Bowser Jr.
Bowser: Son? You’re alive!
Wario: Cork it, scaleface! Ever since he was mistreated he ran away. He looked Waluigi and me up immediately. He told us everything, and now he’s one of us.
Bowser Jr: I’m sorry, Dad, I just had to.
Bowser: Guards set a course for Pipe Land!
They do.
30 minutes later…
Mario, Luigi, Wario, Waluigi, and Bowser Jr. are chained to a pillar in an arena. At the top is an area from which Bowser and the Koopalings (minus Jr) are watching. Koopas from all over are watching the execution. Ludwig, the leader of Pipe Land, gets up and announces.
Ludwig: Let the executions begin!
Several bosses from a lot of games enter the arena. They are Petey Piranha, Goomboss, Topmaniac, King Boo, and Lakithunder.
Bowser Jr: I have a bad feeling about this.
Petey Piranha goes after Mario and spits goop on him, but the goop hardens and breaks the chains, freeing Mario. King Boo tries to ram into Luigi but he jumps so high that the chains break, freeing Luigi. Goomboss tries to ram into Wario but he jumps and Goomboss breaks the pillar, freeing Wario. Topmaniac tries to hit Waluigi but he ducks and has his chains cut. Lakithunder shoots lightning at Jr. but misses and cuts the chains. Now that all the heroes are free, Mario grabs FLUDD and defeats Petey the way he did in SMS. Luigi pulls out the Poltergust 3000 and sucks up King Boo. Wario just stomps Goomboss like a normal Goomba, defeating him. The some thing happens with the other bosses by beating them like they did in the other games. Meanwhile Yoshi is walking slowly behind Bowser before holding an egg to Ludwig’s face.
Bowser: Yoshi, I was expecting you
Yoshi: Party’s over, Bowser.
Bowser: We’ll see about that.
Two Hammer Bros. come from behind and are about to shoot Yoshi, but Shy Guy ships with General Guy and Lewis come and destroy the Koopa minions. They pick up Yoshi, Mario, Luigi, Wario, Waluigi and Bowser Jr, and leave.
Mario: General Guy! What are you doing here?
General Guy: Saving your life! We owe a debt to you since you saved ours.
Mario nods as General Guy and his ships leave the arena. Bowser leaves the arena to track down his son.