Doopliss and Amos woke up in a small holding cell somewhere. They last remembered being attacked by King Boo after losing the battle with the Mario Brothers. Then it had all gone black. The holding cell walls were lined with mold and smelled like mildew. A soft plop of water was heard as it leaked out of the above pipes and landed with a pop sound on the floor.
Doopliss: Amos, how do we get out of here?
Amos: I'm not sure; King Boo appears to have taken my wand.
???: Why look, it's Amos and Doopliss all locked up in a cell. Need some help?
They turned around to come face to face with a Boo. Not any Boo, however, it was Booseph, their comrade that they had been looking for earlier to use as a lie detector for Peach and Bowser's plan.
Amos: Booseph? What are you doing here?
Booseph: Let's see, um... Oh yeah, we're on Konata Isle!
Doopliss: I thought your Boo House didn't serve King Boo.
Booseph: Well let's just say King Boo decided to make us. Anyway, I can help you get out of here!
Amos: Okay!
Booseph went over to the wall and rapped on some bricks in the wall; a portion of the bricks in the wall disappeared, leaving a hole small enough to crawl through.
Booseph: This way!
They crawled through the hole and reached a narrow cave with water leaking from a pipe in the ceiling and green sludge all over the walls. (Green sludge? EWWWWW!) As they passed, Amos noticed a marking on the wall that looks like a triangle with a black line on top.
Amos: I wonder what that means.
Booseph: I'm not sure, but it doesn't look like anything too good. In fact, it makes me shiver looking at it.
Doopliss: Let's keep going.
They walked through the narrow, desolate cave until they reached a door. Booseph tapped on the door and it swung open, pushing the trio to the other side. They looked back to see no door there. They were now in a stone room with no windows and barely lit candles illuminating a tiny area of the room. The light may have been dim, but they could still barely make out their surroundings (except for Booseph, who can see fine in the dark).
???: BLEHEHEHEHE! You! How dare you escape your cell? And you! I trusted you, Boo to Boo. I now see that was a mistake. No matter, now you will face the wrath of KING BOO! BLEHEHEHEHEHE!
The empty room was filled with a glowing light as King Boo appeared in the center, holding Amos's wand.
King Boo: NOW WE FIGHT!
At the MIA located in underground Mushroom City...
We see a room blanketed in white. Two figures sat in metal chairs facing each other. One was a Koopa sporting his usual black suit and sunglasses reflecting the glare of the fluorescent lights off their glossy surface. The other was a Goomba wearing a blue bowler hat. The Koopa was named Bill DeKoopa and the Goomba was reluctant to tell his name.
Bill: Tell me, Goomba, what do you know about the Mushroom City mafia?
Goomba: I tell da secrets of our group to no one!
Bill stood up and took a small, handheld Bullet Bill launcher from its place in his pocket.
Bill: The MIA is not going to tolerate your denial much longer. While I am not allowed to shoot anyone brought in here save someone destroying the place, I might just make an exception for your case. Understand?
Goomba: You threaten me and I no like.
Bill: Well if you were to answer me this gun would resume its place in my pocket, but if not it will keep its place aimed at you!
Goomba: Da boss said if I tell anyone I'll be killed.
Bill: If you tell us now we will put you under a witness protection program until we catch this lunatic. Then you'll join him in prison. We might even place you in another prison separate from his if you're useful. While your charges can't be dropped, it's better than death.
Goomba: You wouldn't shoot me! You're not allowed.
Bill: Watch me!
Goomba: You can stop da boss, but not his boss. He'll stop you!
Bill: That's unlikely. Now SPILL the beans.
And with that, Bill shot the Goomba's foot. The Goomba howled in pain as his foot literally exploded with pain.
Bill: I'll be back in an hour, and if you don't tell me you get a shot right between the eyes.
Bill walked towards the wall, and once he reached it he transmitted right through the wall, jiggling like Jello. He came out on the other side into the heart of MIA, busy secretaries rushing by and agents preparing for missions. He turned around to see a window and a door in the wall not seen on the other side. Looking through the window was a Mushroomer clad in overalls and a white shirt. He walked towards Bill.
Mushroomer: Your methods of getting information don't sit with me, Bill. Do we need to suspend you from the MIA?
Bill: Listen, I do things my way and you do them yours, Russell.
Russell: It's more than that, it's-
Bill: I don't care! Just give me my next operation and I'll be on my way.
Russell: We will deal with this later... Anyways... We've dug deeper into this case and discovered a connection between Todd, this guy, and the attack on Toad Town. They all seem to have someone of a greater power working against us.
Bill: With Todd I think that was on his own accord.
Russell: Apparently not. We dug into the park's phone records and discovered a call from Todd to the Mushroom Mall after you left. The person conquering Toad Town is not the mastermind behind it. We have received transmissions from the tower telling us to stop meddling in her master's affairs. The Goomba in that room... his boss has a higher power. What if this master is the same thing?
Bill: Impossible. No creature of Plit could ever control such powerful beings singlehandedly.
Russell: Who said it was from Plit?
Bill: ...
An awkward silence passed between the two.
Bill: What?
Russell: I don't know, maybe it's an alien. We have had aliens visit Plit before. Tatanga, the Shroobs... Others too. Like that case a few years back with the UFOs. Anyway, whatever this master is, if he has control of the Mushroom City mafia, some freak with a tower cannon, and Todd, he must have immense power.
Bill: If?! You just make conclusions without digging deeper! You need some concrete facts here.
Russell: Whatever is going on here, we need to figure it out.
Just then a Goomba with nerdy glasses and a tie ran up to Russell.
Goomba: Russell, commander sir! We've decoded the prophecy! It isn't good news... Part of it speaks of a retaining force of a great city being wiped out.
Russell: Retaning force... Great city! That could mean-
Bill: US!
Just then a massive explosion rocked the underground fortress. The electricity went out and the monsters of the dark came in...
Meanwhile...
Mario flinched from the oncoming blow just in time to miss it. One of the dragon's green, scaly legs had come back and almost hit him. The dragon swooped E. Gadd up onto its back and forced him into a crevice of its fat body, and began flying in circles. The dragon was trying to throw Mario and Luigi off while keeping E. Gadd on. He swerved magnificently through the air, his wings flapping, pit pat pit pat. Luigi's grip on the dragon's tail began to fade as did Mario's on the dragon's back leg. The dragon swerved right, then did a loop, but Mario and Luigi still hung in there.
Luigi looked down and saw a brilliant landscape beneath him. There was the crystal clear water river flowing out of Wendy's bay. On all sides of the stream were trees of green bearing home to a great many animals. In this forest were open fields in which Luigi spotted animals of enormous preportions. Giant Piranha Plants sat there waiting for prey. Giant Dry Bones hid out on the edge of the clearings away from the bright light. Many other giant creatures roamed this field, giving it spectacular panoramic views.
As Luigi looked down, Mario looked towards the upcoming cliffs on which he could make out a castle with rainbow colors. Apparently, the dragon could too, and it began to fly down towards the castle's tallest tower. As they got closer Mario could make out an opening in the tower that obviously served as the dragon's docking bay. They got closer and closer.
Luigi looked up just in time to see hammers flying towards them from the castle walls. Hammer Bros. were perched there, tossing hammers up into the sky towards the plumbers with perfect speed and agility. Their aim, however, was not perfect. The hammers missed the Brothers and hit the dragon instead. One hit so unfortunately that it smacked into the dragon's pupil, causing the creature to roar in pain. Its flying pattern declined, sending it towards somewhere below the tower's opening. The dragon had no time to recover and hit the bricks, sending it crashing through the wall and into an area like a throne room. Mario and Luigi hit the floor hard, causing immediate pain. Luigi looked up slowly to see Iggy sitting suprised on the throne.
Iggy: That was not how I planned things but... It shall do. Prepare yourselves, plumbers! I will deal with you swiftly and quickly. Mwhahahaha!
In Toad Town...
The Koopas from the MIA teleported to the tower's floating doorstep and swiftly knocked down the door. The tower was a maze of rooms that would take forever to describe, but let's just say the entered and went up a staircase to a giant room that had tons of doors leading in and out of it. Another staircase in that room led up. They followed that staircase to Cackletta's main room, where she sat on a green throne built out of beans.
Cackletta: Who dares enter my domain?
Agent: Put up your hands and we will deal with you swiftly and painlessly.
Cackletta: In your dreams! Eyhaa ha ha ha ha ha HA!
She lifted up her arm and lightning came down on the agents. She then removed the Crystal Stars from her cloak.
Cackletta: Eyhaa ha ha ha ha ha HA!
She kicked aside the throne and behind it was a machine in the wall into which she put the Crystal Stars. A beam of power sprayed from the machine, which was an orb with a blinking red dot and a nozzle. Cackletta glowed with multicolored energy. She then snapped her fingers and disappeared, then reappeared behind the singed agents now carrying Bullet Bill Blasters. BANG! A flash of light came from her hands and then formed into a star-shaped object that then cast Supernova. She then whipped around and disapeared, reapearing behind an agent, then struck them with lightning. She disappeared and reappeared in front of her throne and made holes for the agents to fall through. She then used the Earth Tremor power of the Diamond Star to launch them in the air, only to have them slam back down hard due to the weights that were on them when they came out of the hole like in MLSS.
Fawful: Mistress, it is ready!
Cackeltta: Wonderful! Fawful, bring it here!
Fawful came into the room wheeling a big, arch-like thing on a stand with wheels. The arch was metal and decorated with a rotting, thorny vine, and floating in the center was a black and red dot of energy. Cackletta placed the stars in the energy dot and it zapped her, making her glow with a red energy.
Cackletta: Eyhaa ha ha ha HA!
She began to grow bigger and bigger...
Meanwhile...
Toad had successfully destroyed his clone and the others', but after releasing his friends from their prisons, a tentacle had grabbed his foot and was pulling them down through a hole in the floor into more green essence. Scarvy and Toadette had woken up immediately...
Scarvy: We must be doin' sumpin' or we be stuck down here forever!
Toadette: Uhh... Toad!
Toad: What?
Toadette: T-t-t-turn around.
Toad turned around to see a giant Goomba with tentacles coming from where its feet should be.
Goomba: ROAR! WHO DARES DISTURB MY SLUMBER?!
Toad: AHHHHHH!
Goomba: GET READY TO DIE! I SEE YOU HAVE DESTROYED MY CLONES OF YOU THAT I USE AS MY PLAYMATES AND FOR MY MISTRESS TO USE LIKE A MINDLESS ROBOT... ROAR!
The tentacles let go of Toad and slammed into the floor. They went for the group but Toadette spin-kicked them and they swung back and hit the wall.
Toad: Toadette, spin-kick them at the Goomba this time!
Toadette: Okay!
She did so and a tentacle hit the Goomba's head, knocking him upside down and revealing three glowing red globs that powered him. Toad jumped on one and it burst, making the Goomba turn back right-side up and get angrier. This time it charged them and chased them around the room until Scarvy blew up near him when he tripped and fell underneath the Goomba, bursting another glob. Toadette jumped for its head and spin-kicked it right between the eyes, knocking it on its side. Toad hit another glob, and when it burst the whole Goomba shrank and then exploded.
A door appeared and Toad, Toadette, and Scarvy stepped out into the tower, happy to be in fresh air. They heard rumbling in a nearby room and ran in to see Cackletta getting bigger and bigger...
At the MIA...
The halls were flooded with shrieks as the lights went out.
Bill: What if the containment cells were opened in the power outage?
Russell: I hope not... If they were, they would be all over the agency.
?: OOOOOOOOOOOOOOOOOOOHHHHHHHHHHHHH!
Goomba: W-w-what was that?
Russell: Calm down, Louis, I'm sure that was just the generator coming back on.
Random Screaming Person: AHHHH! MONSTER!
They turned to see floating hot pink eyes in the dark.
Bill: RUN!
They ran away as the random screaming person disappeared into the dark. They ran for who knows how long until they reached a door into which they went. It was the control room and currently sported the only lights in the building, having been equipped with solar lights. Louis ran up to a computer that was still operative and punched in some keys until an image came up on the screen.
Louis: The containment areas are still closed... What's this? There are weird energy spikes in the fusion room... It seems that something or someone is using that room to suck energy from the system. In fact, on the heat vision views I can see of the room, it looks as if they are collecting a large amount of atomic energy in the center tank... Maybe you guys should investigate... I would come, but I should stay here so I can help.
Bill: Fine... Let's go.
They entered the dark hall again and nimbly escaped more pink eyes and reached the fusion room. Russell opened the big, black door with his key, completely ignoring the Do Not Enter sign. They entered the room, which consisted of small, round tanks full of energy on the wall. In place of where a big tank should have been was a big ball of energy. The shadow had fused with the energy and turned around to face them, its big yellow eyes staring at them.
Shadow: What bringssss you here...? Are you ssssssad or mad at me sssssssucking up the energy? I will deal with you! Let the battle begin...
Back with the Marios...
Iggy blasted some magic towards them and they dodged as it exploded, destroying part of the floor big enough for E. Gadd and the dragon to fall through.
Iggy: NO! Blappy!
Luigi: Blappy?
Iggy: MY DRAGON!
Mario: Oh!
Iggy blasted at them some more and began hovering over the hole in the floor. Mario tried to throw a Bob-omb from the suitcase at Iggy, but It didn't work.
Iggy: Ha! Don't waste your time... I'm invincible!
He blasted at them and one of his blasts turned into a magical starburst, a fragment of strong magic that could be picked up and thrown. Mario threw it at Iggy and Iggy flinched.
Iggy: HOW DARE YOU, MARIO?!
Iggy began blasting more than ever and threw Bob-ombs at the few starbursts he could, destroying them. Luigi used his thunder to pull a starburst towards him, and threw it at Iggy. It exploded and Iggy got furious. He than blasted faster and blew starbursts up even faster. Luigi sacrificed himself and grabbed one only to be hurt by a bomb. Mario grabbed the burst and threw it at Iggy, who fell back to the floor hurt.
Iggy: Ow!
Just then Blappy flew through the floor and Luigi and Mario grabbed on again as he flew out of the dark room. As they flew from the castle, the top exploded as Iggy came out riding his doomship...