One day, at Mario and Luigi's house, Mario and Luigi are still in bed. Just then, Toad comes to the house.
Toad: Wake up, guys! The princess is waiting for you!
Mario and Luigi are still asleep.
Toad: WAKE UP ALREADY!
Mario and Luigi are still asleep.
Toad: Fine, I guess I'll have to do this.
Toad pours a bucket of hot water on Mario and Luigi.
Mario and Luigi: HOT! HOT! HOT!
Toad: Finally! You guys are awake!
Mario: Yes Toad, we are awake.
Luigi: But we both got a nasty burn on our backs.
Toad: Sorry! How about a Mushroom?
Mario and Luigi eat the Mushrooms Toad has and recover damage from the burn.
Luigi: Thanks, Toad!
Toad: No problem, guys! Anyway, the princess is waiting for you at her castle.
Mario: Let's-a go!
Mario, Luigi, and Toad head for Peach's Castle. Peach is in the lobby waiting for them.
Peach: Hey Mario, Luigi, and Toad! Are you ready to go?
Mario: Go where?
Luigi: Mario, how could you forget? We are going to Professor E. Gadd's Lab to see his new invention.
Mario: Sorry, I must have not heard about it when we were eating pasta.
Peach: Oh, Mario.
Luigi: That's my brother.
Toad: Don't we have anywhere to go right now?
Peach: That's right! We have to go to E. Gadd's Lab to see his new invention.
Luigi: I said that.
Mario: Let's-a go!
Mario, Luigi, Peach, and Toad head for E. Gadd's Lab. E. Gadd is waiting for them next to an arch-shaped machine.
E. Gadd: Thank you for coming, youngsters. I've got a real treat for you today. It is the Nintendo Portal! Step inside it and you will go to another place in the Nintendo Universe!
Peach: Sounds like fun!
Luigi: Peach, remember the time you used his time machine?
Mario: You were taken by the Shroobs and we had to rescue you.
Toad: We'll get taken by aliens if we go in that portal? COOL! I want to go!
Peach and Toad go though the portal.
Mario and Luigi: OH NO!
Just then, Toadsworth walks into the lab.
Toadsworth: Hello, Masters Mario and Luigi. Have you seen Princess Toadstool?
Mario: She went through the portal.
Toadsworth: SHE WHAT?! Did she learn by now to never play with that scientist's inventions?
Luigi: I warned her about that.
Toadsworth: PRINCESS! WHERE ARE YOU?
Toadsworth knocks himself out.
Toadsworth: (quietly) Princess.
Just then, a Klaptrap (Donkey Kong Country) comes out of the portal.
E. Gadd: What in tarnation is that?!
Mario starts fighting the Klaptrap. He jumps on it, but does little damage.
Luigi: Hey Mario! Want to learn how to damage the monster a lot?
Mario: I guess so.
Luigi: When you are about to jump on it, keep your legs straight to deal more damage.
Mario does this and gets better results. Just then, the Klaptrap bites Mario.
Luigi: Mario! Are you ok?!
Mario: I'm fine, Luigi.
Luigi: Want to dodge its bite?
Mario: If it means not getting bitten, sure.
Luigi: Just jump when it gets near you. If you land on it, you'll do damage.
Mario jumps to avoid the bite and he lands on the Klaptrap to give it some damage. The battle goes on like this until the Klaptrap lies defeated on the floor of the lab.
Luigi: Mario, what do you think that was?
Mario: I have no idea. Did it eat...
E. Gadd: Don't worry, fellas. She wasn't this critter's brunch, but if this is similar to what happened the last time, she got herself kidnapped again.
Mario and Luigi: Oh no!
E. Gadd: Don't worry, boys. You'll save her like you always do.
Mario: Let's-a go!
Mario steps through the portal.
E. Gadd: Aren't you coming, Luigi?
Luigi: Are you kidding me? There may be bad things on the other side of that portal. I'm staying at the house.
Luigi is about to go to the house, but a green ghost (Luigi's Mansion) puts a banana peel on the floor, Luigi trips on it, and he slips into the portal.
E. Gadd: What in tarnation? How did you get out of your canister?
The ghost points to a hole in his canister.
E. Gadd: Whoops, I forgot to patch that up a while back.
Meanwhile at Bowser's Castle, Bowser is formulating a plan to kill Mario.
Bowser: Maybe if I heat up some tar, I will...
Just then, Kamek comes into the throne room.
Kamek: Lord Bowser! Terrible news!
Bowser: Did Mario steal all my tar? Curse you, Mario!
Kamek: It's worse than that!
Bowser: It is? What is it then?
Kamek: Peach is nowhere to be found!
Bowser: What?! I can't believe this! I come up with the best plan to kill Mario and my girlfriend is gone!
Kamek: What should we do?
Bowser: I have the perfect plan. KOOPA KIDS! COME HERE!
The Koopa Kids came into the throne room.
Bowser: Koopa Kids, I have a very important mission for you.
Lemmy: Do we get to use tar too?
Bowser: NO! Your mission is to go to the far reaches of the Nintendo Universe to search for Peach. Wendy will go to DK Island, Iggy will go to Hyrule, Morton will go to the Lylat System, Roy will go to Dreamland, Larry will go to Pikmin Land, Ludwig will go to Pokemon Island, and Lemmy will go to Jiggy Country.
Wendy: I always wanted to go to an island.
Iggy: I bet the wizards of Hyrule will teach me more magic.
Morton: Yes, all right, sweet! I can tell, inform, advise all the people there about my speeches!
Roy: Dreamland? Sounds girly.
Larry: I can raise an army of Pikmin there.
Ludwig: I can do experiments on all the Pokemon.
Bowser: Listen, you are only going out to get Peach so don't get deep in your activities. Got it?
Lemmy: You don't have to worry about that too much because I may be the one to get her.
The Koopa Kids get on their airships and set out to the lands they had been assigned., Meanwhile, Mario is on a very sunny beach on DK Island. Just then, he finds Luigi lying on the sand.
Mario: Luigi, are you ok?
Luigi: I'm fine, Mario.
Just then, Diddy Kong shows up.
Diddy: Hey, Mario and Luigi! Nice to see you guys again.
Mario and Luigi: Hey Diddy!
Diddy: I'd love to catch up on old times, but now's not the time for that! You must come to DK Village with me!
Luigi: What's the problem?
Diddy: I'll tell you when we get there!
Mario and Luigi follow Diddy into the jungle. Meanwhile in Gruntilda's Lair, Gruntilda has Peach in a cage.
Grunty: I've got you, my pretty, and your little friend too.
Peach: Can I leave this dump?
Grunty: You can, but after I make you very ugly!
Peach: WHAT?! I DON'T WANT TO BE UGLY!
Grunty: You don't have a choice in the matter, my dear. Once you're ugly, I can be very beautiful!
Peach: NO! WHAT ARE YOU GOING TO DO TO TOAD?!
Grunty: I don't really want your friend, but Klungo may have a use for him.
Klungo is seen with a knife and a fork. Toad is on a table.
Klungo: Mmmmm. Klungo like Musssshroomssss.
Toad: Great, I came here to get kidnapped by aliens, but I get kidnapped by a witch and I'm about to be food for a green guy.
Lemmy sees what was going on from behind a box.
Lemmy: I found Peach. All I need to do now is wait for the best time to take her.
Meanwhile, Mario, Luigi, and Diddy have arrived at DK Village. The houses are shaped like barrels and they are in the trees.
Mario: So this is DK Village. Where are the other Kongs?
Diddy: The note in Donkey's house will tell you more. You can climb that vine to get there.
Luigi: I don't think I can climb vines.
Diddy: Sorry, wrong game. You can use a jump pad to get up there.
Mario: Let's-a go!
Mario and Luigi use the jump pad to get to DK's house. It has a yellow roof. Inside the house, there is a note pinned to the wall.
Luigi: I wonder what that note said?
Mario and Luigi read the note.
Note: Dear Diddy, I've got the other Kongs on my ship. If you want them back, give me the Golden Bananas. King K. Rool.
Mario: We better go to K. Rool's ship to get the Kongs back!
Luigi: But Mario, what if he is very dangerous?
Mario: Don't worry, Luigi. We faced a lot of dangerous people on our last adventures. We can defeat him!
Just then, a Kremling comes into DK's house.
Kremling: I don't know who you guys are, but I will send you to K. Rool right now!
Diddy: Hey guys, if you jump on his head before you start the battle, you can do some damage to him.
Mario jumps on the Kremling's head. The Kremling takes damage.
Diddy: Hey Luigi, did you know you attack similarly to Mario?
Luigi: I do know that. I reminded him how to battle a while back.
The Kremling is about to attack. Mario is about to jump to dodge his attack, but he attacks Luigi instead.
Diddy: That must have hurt. I know a trick on how to dodge enemy attacks. Want to hear it?
Luigi: If it means not getting hit, sure.
Diddy: You must pay close attention to how he moves before he attacks. If he raises his right fist, he will attack Mario. If he raises his left fist, he will attack Luigi.
Mario and Luigi continue the battle while following Diddy's advice. They win the battle.
Diddy: That must have been a rough battle. Have this magic suitcase.
Diddy gives Mario and Luigi a suitcase.
Mario: What's so magic about it?
Diddy: Put in a Mushroom and see for yourself.
Mario puts a Mushroom in the suitcase and it transforms into a banana.
Diddy: The suit case has the ability to change certain items so they can match the current world's items.
Diddy: The suitcase can also hold gear and check your status.
Diddy: Try eating that banana. It's still works like a Mushroom, but it just has a different taste and shape.
Mario and Luigi eat the bananas that are in the suitcase.
Diddy: Now to take you guys to the beach. I will show you guys how to get to K. Rool's ship.
Diddy leads Mario and Luigi out of the jungle and back to the beach.
Diddy: This is how we are going to go to K. Rool's ship.
Diddy whistles a call and a swordfish swims up to Diddy.
Swordfish: (Hey Diddy! What do you need?)
Diddy: Hey Enguarde! We need to get to K. Rool's ship. Will you help us?
Enguarde takes Mario, Luigi, and Diddy to K. Rool's ship.
Diddy: Thanks, Enguarde!
Enguarde: (Any time, Diddy!)
Enguarde sinks back into the sea.
Diddy: The other Kongs are below deck. We need to find a way to get under there.
Luigi: I guess this may take a while.
Luigi walks around deck. Just then, he falls through a trap door that leads under the deck.
Diddy: Luigi just found a way to get below deck! Good job, Luigi!
Mario and Diddy go through the trap door. They are under the deck.
Diddy: We need to find the ship's hold. It has the key to the Kongs' cage that is somewhere below deck.
Mario: Do you know the way to the hold?
Diddy: I sure do. I know this ship very well because I explored it once.
Diddy takes Mario and Luigi to the hold. The door is guarded by Klump.
Klump: Hey! I heard that you two killed a Kremling! If you guys are that tough, I'll challenge you two to a fight!
Mario and Luigi start fighting Klump.
Diddy: Guys! This is a very tough member of K. Rool's army! I have some barrels for you guys to make the battle easier!
Diddy gives Mario and Luigi barrels.
Diddy: Try kicking around a barrel as if it were a shell.
Mario and Luigi kick around the barrel like a Red or Green Shell in Mario & Luigi 2. Klump throws some Oranges at the brothers. Mario and Luigi dodge the Oranges. Mario and Luigi keep kicking their barrels, and they defeat Klump. Then Mario and Luigi walk into the hold. It has floating barrels with question marks on them and there is a key on the floor. Diddy picks it up.
Diddy: Finally! We got the key to the cage! I'll take you to it, guys!
Mario: What's with the floating barrels?
Diddy: The barrels are like the blocks you find in the Mushroom Kingdom. Each land has its style of block. Those barrels can be hit easily, but if you find red or green blocks, you need to hit them with the right brother. Red blocks can be hit by Mario and green ones can be hit by Luigi.
Luigi: I get it.
Mario: Me too.
Mario and Luigi grab all the goodies from the barrels. They now follow Diddy to the cage room. The door is blocked by Krusha.
Krusha: I heard that you guys defeated a lot of things, but I bet that you can't defeat me.
Mario and Luigi are fighting Krusha. Mario and Luigi attack him with all the tricks they learned. Just then, Krusha performs a shockwave attack that the Brothers have trouble dodging. This attack does heavy damage to Luigi and knocks Mario out.
Diddy: That attack knocked Mario out! Use a balloon on him!
Luigi: How will a balloon help?
Diddy: Balloons are like 1-Up Mushrooms. Use it on him!
Luigi uses a balloon on Mario. He is now on his feet again.
Diddy: That attack did some huge damage to you guys. Eat a banana bunch. It works like Mushroom Drops.
Mario and Luigi eat a banana bunch. It healed their damage.
Diddy: If you guys jump at the same time, you can dodge Krusha's shockwave!
Mario and Luigi use the advice to dodge all of Krusha's attacks. They defeat Krusha.
Krusha: You guys are tougher than I imagined! I better get stronger if I want to beat you guys!
Krusha runs off to the gym. Mario, Luigi, and Diddy enter the cage room. The Kongs are in a cage.
Dixie: Diddy! You came to rescue us!
Funky: I knew you could do it, little dude!
Diddy: Thanks, but I did have a little help from Mario and Luigi.
Cranky: Get us out of this cage now! I have other things to do!
Diddy unlocks the cage and Cranky hits Mario with his cane.
Cranky: That was from being mean to me in Donkey Kong!
Diddy: We saved the Kongs! Hey, where's Donkey?
Dixie: K. Rool has him in a cage in his quarters.
Mario: Don't worry! We'll get him back!
Luigi: Because we're the Mario Brothers!
Diddy: Great! His quarters are down the hall.
Mario and Luigi head for K. Rool's quarters. Inside his quarters, K. Rool is in front of Donkey Kong's cage.
K. Rool: I'm such a genius! I kidnapped all the Kongs this time, and I left Diddy to make the choice of giving the bananas to me!
Donkey Kong: You won't get away with this, K. Rool!
K. Rool: What makes you think that?
DK: Mario and Luigi are here!
K. Rool: Mario and Luigi?! Ha, ha, ha, ha, ha! Don't make me laugh! Mario and Luigi will never come here because they go on too many adventures that involve defeating Bowser and saving Princess Peach! That makes them too busy to save you! What makes you think that they will save you!?
DK: They are behind you right now.
K. Rool: Behind me?! Ha, ha, ha, ha, ha! You come up with the best stories!
Mario: Maybe we can take DK while K. Rool is distracted.
Mario and Luigi sneak past K. Rool, but Luigi accidentally steps on his tail.
K. Rool: Ouch! Hey! Who did that?!
K. Rool turns around to see Mario and Luigi.
K. Rool: How on Plit did you guys get here?! I thought you guys were on an adventure to save Princess Peach again!
Mario: We are! Do you have her?
K. Rool: Do you think that a non-Mario villain would steal a Mario character?
Mario: It's possible.
Luigi: Can you give her back?
K. Rool: I don't have her. Now beat it!
Luigi: We won't go until we get DK out of that cage!
K. Rool: You want that monkey too? If you want to have him, you got to fight me for him!
Mario and Luigi start battling K. Rool. Mario jumps on K. Rool's head but gets hurt due to the crown on his head.
DK: Careful Mario! If you jump on some spikes, you will get hurt!
Luigi: How will we attack him?
DK: You can try to find a weakness.
Mario: Let's try jumping on his belly button!
K. Rool attacks by rolling his crown. Mario and Luigi dodge it. They jump on K. Rool's belly button, and his crown falls off. Mario and Luigi jump on his head. K. Rool is defeated.
K. Rool: I can't believe I was defeated by some plumbers!
DK: I told that the Mario Brothers are here!
K. Rool: You may have won this time, but next time, I will be better at fighting!
K. Rool runs off. Mario and Luigi open DK's cage.
DK: Thank you, Mario and Luigi! You saved me from the clutches of K. Rool. Maybe I can return the favor sometime.
Mario: Right now, we have to get back to DK Island.
Above deck, Enguarde is waiting for Mario, Luigi, and Diddy. Just then, the Mario Brothers and the Kong Family jump on deck.
Diddy: Hey Enguarde! We need you to take us back to DK Island.
Enguarde: (OK, but it may take a while.)
Later, back on DK Island, Enguarde has just delivered the last of the Kongs.
Enguarde: (I did it, but it took me a long time to do.)
Diddy: Good job, Enguarde! You need rest!
Enguarde sinks back into the sea.
Diddy: If you want to know where Peach is, I don't have the slightest idea.
Dixie: Hey Diddy! What's that on top of the island?
Diddy: It looks like a ship.
Luigi: Maybe Peach is there.
Diddy: If you want to get up there, you must learn two tricks that will help you get up there. Dixie, will you help me teach the Mario Brothers our tricks?
Diddy: Let me take you to the training island.
Diddy and Dixie take Mario and Luigi to the training island. The island has two parts to it. One part has a hill in the shape of a staircase with high steps. The other one has huge gaps.
Diddy: The first trick is a high jump. You can use it to scale high ledges. First, Mario has to jump on Luigi.
Diddy jumps on Dixie and squishes her.
Diddy: Then, Mario will jump.
Diddy jumps, Dixie gains her shape, and Diddy jumps high in the air with Dixie holding on to his legs. They land on one of the ledges that make up the hill.
Diddy: That's all there is to it. Try it out!
Mario and Luigi perform this move on each of the ledges. They are now at the top of the hill with Diddy and Dixie.
Dixie: Good job, guys! Time to learn my move!
Mario, Luigi, Diddy, and Dixie are now in the other area.
Dixie: The next trick is a spin jump. You can use it to cross wide gaps. First, Luigi has to jump on Mario.
Dixie jumps on Diddy.
Dixie: Then, Luigi will spin.
Dixie spins. This causes Diddy to spin. They are now floating. They float over one of the gaps.
Dixie: It's easy to do. Go ahead and do it!
Mario and Luigi perform this move on each of the gaps. They are now across the last gap with Diddy and Dixie.
Diddy: That was pretty good, guys. If you run into any twisters while spin jumping, you can get a boost on your spin jump. Now you are ready to explore the ship on top of the island!
Diddy and Dixie take the Mario Brothers off the training island.
Diddy: You guys check out the ship, we'll go take a rest in the jungle.
Diddy and Dixie head back to the jungle.
Luigi: Who do you think that ship belongs to?
Mario: I have a hunch.
Mario and Luigi use their new tricks to get to the top of the island and always use a twister if there was one near by. Mario and Luigi get to the top of the island. Wendy's airship is there.
Mario: I knew it! Wendy's airship is here!
Wendy gets off her airship.
Wendy: I can't wait to hit the. MARIO AND THAT GREEN GUY?!
Luigi: Why do people do that to me?
Mario: Where is Peach, Wendy?!
Wendy: How should I know? I'm on a search for her, but I really want to hit the beach. See ya!
Wendy heads for the beach. Mario and Luigi follow her. They find her sitting in her beach chair while the Kongs feed fruit to her.
Mario: We got to save the Kongs from Wendy before she makes them her slaves forever!
Wendy: What are you guys doing here? Can't you see that I'm on vacation?
Luigi: We want you to stop making the Kongs slaves.
Wendy: Listen here. I had to do all kinds of things and I never get any rest. Leave me alone.
Mario: Not until you free the Kongs!
Wendy: If you want the Kongs so badly, you have to fight me for them!
Mario and Luigi fight Wendy. Wendy attacks by throwing red and green life savers. She also attacks by breathing fire. Mario and Luigi attack by jumping and using barrels. They did us a banana or two somewhere in the middle of the battle. They defeat Wendy.
Wendy: WAAAAAAAA! WAIT 'TIL I TELL MY DADDY!
Wendy runs off and she drops a key with Bowser's head on it.
Mario: We defeated Wendy O. Koopa!
Luigi: Mario, what is that key thing?
Mario picks up the key.
Mario: I don't know, Luigi. We can show it to E. Gadd.
Dixie: You saved us again! How can I ever repay you two?
Luigi: Maybe we can use her to make Toadsworth happy.
Mario: What do you mean?
Luigi whispers something in Mario ear.
Mario: I get it now. Dixie, we need you.
Dixie: For what?
Later, Mario and Luigi are back at E. Gadd's Lab. Dixie is dressed as Princess Peach.
Toadsworth: Let me get this straight. You have been transformed into a monkey?
Dixie: That's right.
Toadsworth: I'm very sorry to hear that. Let me make it up by giving you all the bananas you can eat.
Toadsworth feeds Dixie a lot of bananas.
E. Gadd: Hmmm. Very interesting.
Mario: Do you know what it is?
E. Gadd: I sure do, fellas. It's a key to Bowser's Castle. If you get all seven, you can get into Bowser's Castle.
Mario: We should go to the other Nintendo Worlds and get the other keys.
E. Gadd: That may be a good idea. You should go check Hyrule. I think another Koopa Kid may be there.
Mario: Let's-a go!
Mario and Luigi walk through the portal again. Meanwhile at Bowser's Castle, Bowser is on his throne. Just then, Wendy comes into the room.
Bowser: What is it, Wendy?
Wendy: It's those Mario Brothers! They beat me again!
Bowser: The Mario Brothers are out looking for Peach too?! Don't worry, Wendy. Your brothers will get rid of them.
Wendy goes to her room to rest.
Bowser: Those Mario Brothers are annoying as ever! I hope that my remaining children can get him!