Back in the Mushboo Kingdom, Mario and Luigi are seen running into the castle. Inside, they meet up with King Boo, Princess Boo, and Prof. Boo.
King Boo: So, no sign of Booster?
Prof. Boo: Negative, sir. I have sent some minions toward the wreckage to see if we can find any trace of him. Until then, we have no general.
King Boo: Very well. Dismissed!
Prof. Boo leaves and King Boo turns to Mario and Luigi.
King Boo: So?
Mario and Luigi hold up the crystal ball they got from the Star Spirits. Then, smoke engulfs them and in their place are Booario and Booigi.
Booario: We are now able to find the Crystal Hearts.
King Boo: Excellent. Bring it over here.
Booario and Booigi take it and put it down in front of King Boo and Princess Boo. King Boo then turns to Princess Boo.
King Boo: My magic isn't strong enough. Would you mind helping me?
Princess Boo: Of course I will.
They both their stubs on the glass ball and it begins to let off an eerie glow. Then, an image appears. It has a dark background, sandy terrain, and is filled with water. A ship is seen stuck in the sand.
Booario: ... What is that place?
King Boo: That looks like... The Sunken Ship.
Booigi: Great, we get to go underwater.
King Boo: I would send Booster, but he is lost somewhere, so you two are going to go collect it.
Booario: Okay, but why do you need them? I thought you said that the Crystal Hearts turn Peach back to normal.
King Boo: Hehehe. I don't plan to use them the way they are supposed to be used. More will be told in the future; now, get that Crystal Heart!
Boo Bros: Yes sir!
Up in Star Haven, the Koopa Cruiser lands as some Star Kids run and hide, but they notice Mario and Luigi coming out and are somewhat relieved. The heroes head for the Star Sanctuary and confront the Star Spirits.
Eldstar: Mario? What are you doing back? I thought we gave you what you needed. And why do you have Mallow and Bowser with you?
Mario: ... What are you talking about, Eldstar? We just got here.
Eldstar: No, you were here not too long ago. You said you had to stop King Boo and save Peach and the Mushroom Kingdom.
Luigi taps Mario's shoulder.
Luigi: Mario, something's fishy here. I think King Boo has something to do with this.
Mario turns back to the Star Spirits.
Mario: How can we prove to you that we weren't here before?
Misstar: Show us the crystal ball we gave you to locate the Crystal Hearts.
Mario looks at the others and they shrug.
Mario: What are you talking about?
The Star Spirits look at each other. Then a mini star flies in and circles around them all. Mario and Mallow look at the star and begin to realize that they have seen this star before.
The star spins around them, like it’s jumping for joy.
Eldstar: ... You are telling the truth.
Kalmar: Are you sure, Eldstar? How do you know they are not Boos incognito?
Eldstar: Because, Geno would know the real Mario.
He turns to Mario.
Mario: We are sorry we did not believe you. Unfortunately, we already gave the one thing that helps locate Crystal Hearts to your doppelgangers.
Mario hangs his head.
Muskular: But, there is someone else who possesses the ability to locate Crystal Hearts.
Mario: Great... I just wish I knew where he is. After King Boo took over the kingdom, the Boos chased everyone out of Toad Town.
Eldstar: I do believe he doesn't know about this…
Klevar: Yes. A little while back, Merlon said he was going to visit Merle in Starborn Valley.
Mario: Thank goodness. Well, we must be off.
Eldstar: Good luck, Mario.
Mario and Co. turn to leave. But from behind, Geno floats and remains motionless. He then heads back to Star Haven and heads inside a house. Inside is the same doll he possessed back in RPG. He spins around it and a great light appears around the doll. Geno jumps into the doll and the doll begins to grow. The light then fades and Geno is seen.
Geno: ... Time to catch up with Mario.
Geno rushes off toward the Koopa Cruiser. He notices everybody getting on. He starts running faster. Mario is the last to get on. Just as he is about to shut the door, Geno jumps into the door, crashing into it. Mario opens the door and sees Geno on the floor.
Geno gets up and brushes himself off.
Geno: Yeah, it's me.
Mario: You want to come with us, don't you?
Geno: It has been a while since I had some action, so yeah.
Mario: Hop in.
Geno rushes onboard, and the Koopa Cruiser heads off for Starborn Valley.
Booario and Booigi are seen high in the skies over Seaside Town. They fly down and head for the sea. They enter the cave that leads to the Sunken Ship and follow the path to the ship. They eventually reach the outside and find the Sunken Ship. They head underwater and enter. Inside, they look around and find many Greapers and Dry Bones.
Booario: This shouldn't be too hard.
Booario advances, but Booigi stops him.
Booigi: Wait, we can use these guys for our own good.
Booario: What do you mean?
Booigi: Well, they are ghosts except the Dry Bones, but we have a bond with them. If we can talk them into attacking those annoying Mario Bros, we can get that Crystal Heart with ease.
Booario: ... I like it. Let’s try it out.
Booario and Booigi turn to them and approach.
The Koopa Cruiser lands outside of Merle's house, and Mario and Co. exit and knock on the door. It opens and Merle appears.
Merle: Mario, what a surprise. And you brought along friends and... Bowser? Anyway, what brings you to Starborn Valley?
Mario reaches into his pocket and pulls out the Crystal Heart. Merle is amazed at what he sees.
Merle: It's... a Crystal Heart! MERLON! YOU HAVE TO COME SEE THIS!
Merlon slowly walks toward the door and notices Mario holding the Crystal Heart.
Merlon: Ah, all of you have finally come.
Mario: How did you know we were coming?
Merlon: Mario, I have seen this day coming for many years.
Luigi: How is that-a possible?
Merlon: I read a book about the Crystal Hearts a long time ago. Next to the Crystal Stars, they are very powerful. There is actually a prophecy to be told. But please, come in and warm up. Merle, get these fine gentlemen some hot chocolate.
Mario and Co. enter the house and gather around the fire. Merle then brings them hot chocolate except for Geno, as he is a doll.
Merlon: This prophecy was told many years ago, back when the Crystal Hearts were created. It was told by the great powerful Merler. He had created the Crystal Hearts for good. Back in his time, there was a great, powerful, evil ruler known as Booshido. Booshido was a very powerful Boo who was able to perform powerful martial art attacks. He had ten lackeys: a Tanoomba, Duplighost, Shy Guy, Yoshi, Dry Bones, Lakitu, Blooper, Shroob, X-Naut, and Boo. Booshido always sent them to the village he ruled to cause chaos. Booshido's lackeys always caused havoc for the villagers, except for Merler. They knew he had powerful magic to beat them…
Merlon: Merler was fed up with the random attacks on the village, so he created the Crystal Hearts in hopes of stopping him. When he finished, Merler confronted Booshido and used the eight Crystal Hearts’ power to destroy him. Unfortunately, thanks to his Duplighost lackey spying on Merler while he was working on the Crystal Hearts, Booshido knew what was coming. So he used his powers to steal the Crystal Hearts away from Merler. Booshido had used his power to turn the Crystal Hearts dark. He then used them to destroy Merler…
Merlon: But, there was a ray of hope. His younger brother Merlan was working on something else: the seven Crystal Stars. They had much more power than the Crystal Hearts. Merlan confronted Booshido and challenged him. Merlan and Booshido went at it for almost a whole day. Then Merlan pulled out the Crystal Stars and used their power to defeat Booshido and his lackeys. But Booshido used the Crystal Hearts on Merlan. Unfortunately for Booshido, the Crystal Stars had more power and destroyed the darkness within the Hearts, and he froze Booshido and his lackeys in time. Merlan had to protect the Crystal Stars because they are more powerful than the Hearts, so he scattered them across Rogueport. He kept the Hearts, but a few days later, he had a vision of the future, which is now our time period. He saw the King of Boos trying to gather the Hearts for his own evil plan. Merlan could not let that happen, so with a wave of his arm, he scattered the Hearts across the Mushroom Kingdom, hiding them very well…
Merlon: He tried to see more, and more he saw. He saw seven heroes: two of them being plumbers, a cloud prince with powerful magic, a star with many powers, an evil king, and the other two are a mystery. All he found out was that those two were ghost-like. He knew that they would be able to stop the King of Boos from using the dark power of the Crystal Hearts, so he scattered them across the Mushroom Kingdom. Later, he found out that a couple of the Crystal Hearts had been found, but not used for evil. Merlan granted those that found them the rank of guardians. There are seven guardians, but I was only able to track down three. They are Czar Dragon, Tubba Blubba, and Johnny.
Mario: Well, we defeated Czar Dragon, so the other two guardians that we know are Tubba Blubba and Johnny.
Mallow: I suggest we go and ask Johnny first. We haven't seen him in a while.
Geno: I agree with Mallow.
Bowser: I don't care where we go.
Mario: Okay. Off to the Sunken Ship!
Merlon: Good, now, I will try to search for more guardians and give you a call if I find out anything. Do any of you have a calling device?
Bowser: Here, I'll give you my number.
Bowser gives Merlon the number and Merlon writes it down.
Merlon: Thank you. Now, good luck!
Mario and Co. head off to the Cruiser and fly toward the Sunken Ship.
Booario: Hehehehehe! Your plan worked, Booigi.
Booigi: It sure did, Booario. Now, let’s get moving.
Booario and Booigi advance further into the ship. But secretly, someone is watching and following them. It is a Blue Bandana.
Blue Bandana: What are they doing here?
He continues to follow. Eventually Booario and Booigi make it to the puzzle room.
Booario: Nobody told us we had to answer a question!
Booigi goes up to a sign and reads it.
Booigi: These are very valuable to a pirate and can be found at the bottom of the ocean.
Booigi looks around and sees six floating blocks.
Booigi: ... Got it! Booario, hit those blocks until they show the letters P, E, A, R, L, S.
Booario does what he was told. He spells the word Pearls and the door opens.
They rush in, but the Blue Bandana laughs.
Blue Bandana: Hehehehe. They will never get past King Kalimari.
The Koopa Cruiser lands near the cave that leads to the Sunken Ship. Mario and Co. exit and head into the cave. They eventually make it to the ship and head inside. When they enter, everything looks the same as the last time Mario, Mallow, Geno, Bowser, and Peach visited. They head through the first door and are ambushed by Greapers. Bowser breathes fire at them, and the Greapers rush off.
Mario: I forgot about those guys.
Mallow: Don't look now, but there are more coming this way!
Mallow is right. They see Greapers and Dry Bones. Mario and Luigi lunge at the Dry Bones and smash them to pieces with their hammers. Mallow and Geno use their Sonic Symbols and Star Gun to send the Greapers off.
Luigi: Mario, you said that those Greapers are a little like Boo Guys, like they are shy. That doesn't look shy to me!
Mario: I don't know what's going on.
Mallow: I wonder if King Boo has something to do with this.
Geno: It is possible. I mean, they are ghosts.
Bowser: Who cares? As long as you have me, you'll be safe!
Mario: Gee, thanks Bowser.
They go further into the ship. They meet up with more Greapers and Dry Bones, along with a couple Ally Rats, but they manage to beat them. They eventually make it to the puzzle room. Mario looks around and sees that the door is already open.
Mario: Oh no.
They rush in and notice a Blue Bandana tending to King Kalimari’s injuries. The Blue Bandana turns and notices Mario.
Blue Bandana: Oh, Mario! Thank goodness you're here. It was awful!
Mario: What happened?
Blue Bandana: Well, I was patrolling the ship when I came across two Boos, one red and one green. They talked the ghosts into destroying you when you came in. Then they made it to the puzzle room and got the right answer. They came across King Kalimari and beat the tar out of him. Then they left. I don't know how far they are now, but they could have reached Johnny.
Mario: Booario and Booigi, they are the ones who are in here. Come on, guys, we have to go!
Mario and Co. jump down the hole to the lower part of the ship. They rush past everything until they come to Johnny's room. They bash down the door and see a battle going on, the Boo Bros. and Johnny. The Boo Bros. turn invisible every time Johnny launches an attack. Then Booario forms a fireball and shoots it at Johnny. Johnny blocks it with his trident, but it catches on fire. He swings it at them, but they turn invisible. Then the Boo Bros. fire a stream of red and green flames. They hit Johnny, and he is down for the count.
Booario: Take that!
Booigi: Now hand over the Crystal Heart.
Johnny: ... I would... but... it's not... here!
Boo Bros: WHAT?!
Mario and Co: WHAT?!
The ghosts turn around and see Mario and Co.
Booario: I knew that those ghosts weren't going to cut it.
Booigi: Who cares?! We have bigger problems!
He turns to Johnny.
Booigi: All right, where is the Crystal Heart?
Johnny: Some... Smorg came... along and... took it.
Mario: Wait, do you mean, like, a little Smorg?
Johnny: Yeah... Then... I gave chase... but it gathered up more... and turned into one... big Smorg with three tentacles. That is... when I knew... I couldn't... win.
Suddenly the ship starts to rumble.
Luigi: What's happening?
Johnny: It's... back.
Then a giant tentacle breaks through and grabs Booario and Booigi. Water starts to flood the ship.
Mario: We have to get out of here!
Luigi: But what about Johnny?
Johnny: I'll be fine. Just go and beat it!
Everyone but Johnny is able to get out of the ship. They reach a jump panel and land on it, getting bounced out of the ship and onto land. When they reach the outside of the ship, they see a giant Smorg that looks like the one Mario fought in PMTTYD, only the black is replaced with a blue. In the center they find the blue Crystal Heart, along with Booario and Booigi in the tentacles.
Mario: If we want that Crystal Heart, we have to beat it!
Bowser: Finally! Time for some action!
BOSS BATTLE: Sea Smorg
Mario grabs his hammer and lunges at the Sea Smorg, but the Sea Smorg jumps up and lands in the water, camouflaging itself. Mario looks in the water but can't find a thing. Then a tentacle comes up and slaps Mario. Mario is sent into the wall. Luigi tags in and leaps toward the tentacle. He hits it and it rolls back up into the water. The Sea Smorg then floats up out of the water and uses the power of the Crystal Heart to gain a new ability. Its eyes glow red and Booario and Booigi are put right in front of them. Then the Sea Smorg sends out rings of hypnotism to hypnotize the Boo Bros. The Boo Bros. become the Sea Smorg's puppets. Sea Smorg talks to the Boo Bros. in its own tongue, which Mario & Co. cannot understand. Unfortunately, the Boo Bros can. They nod and turn to Luigi and the others. They start firing red and green fireballs at them. Luigi jumps and rushes behind a rock.
Bowser: Some hero.
Bowser charges toward the Boo Bros. and unleashes his own fire breath. The fireballs and breath collide, and Bowser's is more powerful. The breath hits the Bros. and burns them. Mallow then jumps in and uses Sonic Symbols to annoy the Boo Bros. Geno jumps in the air and fires the Geno Beam. The Boo Bros. are hit and are almost down. Mallow finishes with a thunderbolt. The bolts hit the Bros, who are crisped and fall into the water, unconscious. Sea Smorg flings himself out of the water and onto land. He makes all his tentacles disappear and makes three claws appear. Luigi looks from around the rock and screams in terror.
Luigi: AHHHHHHHHHHHHHH! MARIOOOOOOOOOOOOOOOOO!
Mario slowly opens his eyes and notices Luigi scared, and the other three trying to fight off the Sea Smorg.
Mario: Looks like old Smorg learned a new trick. But that won't stop me. Come on, Luigi, I need your help.
Luigi slowly stops shivering and gathers up all his bravery and charges alongside Mario. Sea Smorg notices them and sends one of the claws over to them. Mario and Luigi do a series of jumps to avoid it. They eventually jump onto the arm of the claw and run along it. Sea Smorg tries to shake them off, but doesn't succeed. Mario and Luigi eventually reach the Sea Smorg's core. They start hammering the area and Sea Smorg roars in pain.
Sea Smorg: SSSSSMMMMMMMMMMMOOOORRRRRRGGGGGGGGG!
Mario: Geno! Fire a Geno Blast!
Geno nods and raises his arms.
Geno: GENO BLAST!
Mario and Luigi jump off and colorful blasts are sent down on Sea Smorg. He roars again.
Mario: Bowser, throw him into the sea!
Bowser looks at him and turns back to Mario.
Bowser: I don't know if I can lift something that big.
Mario: Geno, give him a boost!
Geno nods and uses Geno Boost to raise Bowser's power. Bowser gets bigger muscles and walks toward Sea Smorg, picks him up with ease, and throws him into the sea.
Mario: Mallow, finish this with a shocker on the water!
Mallow: You got it!
Mallow summons a lightning blot and makes it hit the water. From underneath, Sea Smorg gets badly electrocuted along with Booario and Booigi, who are launched into the sky without notice. Sea Smorg starts shaking and bursts into a million Smorgs that are sent flying. The Crystal Heart is sent into the sky and lands back in the ocean.
Mallow: We beat that Sea Smorg thing, but the Crystal Heart landed back in the sea. How are we going to find it?
Just then the Crystal Heart is sent up out of the water and lands in front of Mario.
Then a shark jumps out of the water and lands in front of the heroes.
Johnny: Good job, guys.
Luigi: Johnny?! But, how did you survive?
Johnny: Well, after those rotten Boo Bros. beat me and I told you I'd be all right, I fainted for awhile. When the ship flooded, I was able to survive because I am, of course, a shark, but after Mallow sent a shocker into the water, that jolt got me up. I was able to find the Heart, so I brought it up as a thank you. That Heart is yours. Good luck finding the other Hearts.
Johnny jumps back into the water. Mario takes the Blue Crystal Heart and adds it to their collection.
Mario: Great, now we only have six more to go.
Luigi: I suggest we go and get the one from Tubba Blubba.
Mario: Good idea. Let’s get back to the Koopa Cruiser.
Mario and Co. leave the beach and head for the Cruiser.
Back on the Cruiser, Kamek is taking a nap, when a siren goes off and he wakes up.
Kamek: What's going on?! I was taking a nap!
Koopatrol: Sorry, sir, but we have a call from Bowser's Keep.
Kamek: Put it on screen.
A big screen appears and Lemmy appears on the screen. Behind him, the Keep is in ruins and banging is heard.
Kamek: Lemmy? What's going on?
Lemmy: Where's Dad? I need to talk to him.
Kamek: What's happening?
Lemmy: The Keep, it's being attacked by... Wait, what are you? NOOOOOOOO!
The screen goes blank.
Kamek: Lemmy? Lemmy!
Laughter is heard. The screen turns back on and a Boo with red eyes and a jester hat appears.
Booster: HAHAHAHAHAHAHA! Yes, it's me... BOOSTER! I'm back, and I have taken over Bowser's Keep! Come and save it if you dare!
The screen turns off and Kamek begins shaking. Then, Mario and Co. enter.
Bowser: All right Kamek, to Gusty Gultch!
Kamek doesn't answer.
Kamek turns to Bowser.
Kamek: ... Booster is back. He took over the Keep.
Mario and Co. all have shocked faces.