Ponymon Girls: Shades of Harmony

by Lucky Ness

Rating: everyone
Tags: Crossover, Human, Fluttershy (EqG), Other, Adventure, Equestria Girls
Length: 8589

Fluttershy must defeat the Legendary Birds and Mewtwo with her new Pokemon friends.

This story takes place in the same time line as EquestriaBound Girls: Nightmare in Magicant and is a sequel to Pokeshy and Fluttermon from EquestriaBound Girls: Short Stories

Fluttershy is given a challenge by Mewtwo after she befriends a Pikachu and captures a Charizard that came through the portal. Now she must defeat and capture the Legandary Birds to prove her worth to Mewtwo.

Cover art was found here. https://mlpforums.com/user/29961-coco-before-pommel/?tab=reputation&app_tab=forums&type=given&st=825. I have no idea who made it.

Published 2016-11-15 01:10:02 UTC
Last updated 2016-12-20 16:46:43 UTC

Prankster

Author's Note

Credit goes to lunarderpy1 for Articuno's location.

Prankster

-The Next Morning-

FLuttershy wakes up to a soft slapping sensation on her face. She sees a pink creature standing on her chest as her eyes slowly adjust to the lighting.

"Jiggly!"

"What's a Jigglypuff doing in my room at," Fluttershy looks at her bedside clock, "5 in the morning?"

"Jigglypuff!" The Jigglypuff jumps off of her bed and lands on the table, pointing at the note she found yesterday.

"Yes, I know about the challenge." Fluttershy says as she gets out of bed, taking care not to disturb the marker or the microphone located there.

"Jiggly!" The Balloon Pokemon jumps over to her backpack, opens it and reaches inside.

"What is it you need?" The kind-hearted girl asks as she walks over to her backpack.

"Puff!" Jigglypuff says as it emerges from the bag with a Poke Ball before jumping back onto the bed.

"You want to come with me?"

The Jigglypuff nods before dropping the Poke Ball and grabbing its microphone and its marker.

"Puff!" It says as Fluttershy picks up the ball and tosses it at the creature. The ball shakes three times before a star emerges. Fluttershy walks over, picks up the ball, and puts it with her other Pokeballs.

"Now to get ready." Fluttershy says as she heads to her dresser and pulls out her usual white shirt and the green skirt with the butterflies on it before heading to the bathroom to wash up. The moment she sees herself in the mirror, she notices something that looks like the outline of butterfly has been scribbled on her face.

"Well, I guess that explains the marker." She says as she turns the sink on and starts to wash her face.

"So I have to capture Articuno, Zapdos, and Moltres." Fluttershy says, looking at the back of the note as she closes the front door behind her. "It says here that Articuno is in the Canterlot Skating Rink, Zapdos is in the abandoned power plant, and Moltres is in the Everfree Forest." She considers the three Legendary Pokemon and their locations and eventually decides that Zapdos would be the easiest one to go after first. After all, the power plant's within walking distance.

Fluttershy gets her bike out of the garage, then sets off for the power plant with Pikachu and Jigglypuff, who had been scolded for drawing on Fluttershy's face, following close behind her.

Power Plant (VS. Zapdos)

"Well, we're here." Fluttershy says as she turns her bike into the abandoned parking lot, seeing eighteen Pokeballs on the ground in groups of three, as well as a red rectangular device with a small black device on top of it. She was about to walk over to the Pokeballs when she feels something pulling on her leg. She looks down and sees Pikachu with a piece of paper in its mouth.

"Thank you," She says to Pikachu as she takes the paper out of its mouth and starts to read it.

'Seeing how you were never officially introduced to the world of Pokemon, so I've decided to give you a fighting chance. I'll give you a Pokedex and Exp Point Share, as well as let you choose a starter Pokemon. You may only choose ONE, so choose wisely!

-Mewtwo'

Fluttershy flips the piece of paper over and sees a map, showing which Pokemon is in which Pokeball. Fluttershy uses the map to head towards the third Pokeball in the fourth group of three.

"I'll take this one," She says as she reaches down and picks up the Pokeball. Upon doing so, the paper in her hand disappears, as do the other seventeen Pokeballs. She hears a rustling noise and looks down to see another piece of paper. She picks it up and reads it.

'Good choice. Raise it right, and that Piplup may one day be a major threat to me.

-Mewtwo'

Fluttershy lets the Piplup out of its Pokeball and heads to the door of the abandoned power plant with her Pokemon following close to her heels. Upon entering the plant, Fluttershy is bombarded by gale force winds as Zapdos flies down from its perch high in the power plant.

"This is it. Go, Pikachu!" Fluttershy yells as Pikachu jumps forward and uses Thunder. Zapdos dodges the attack and counters with Drill Peck. As Zapdos is attacking it, Pikachu uses Thunder hitting it while it's distracted. This causes Zapdos to let out a screech and flies back a distance before it uses Discharge, unleashing a quick ball of electricity at Pikachu. Pikachu dodges and uses Volt Tackle, engulfing itself in electricity as it runs at top speed at Zapdos, tackling it. Pikachu and Zapdos are both flung by the force of the attack. However, Pikachu doesn't get up.

"You did your best, Pikachu." Fluttershy says as she returns Pikachu to its Pokeball and turns to Jigglypuff. "Jigglypuff, you're up!"

"Jiggly!" Jigglypuff says as it uses Double Edge and flings itself at Zapdos in a life-risking tackle. Jigglypuff collides with Zapdos, knocking it backwards. Zapdos attacks with Ancient Power, flinging stones at Jigglypuff. Jigglypuff dodges and sings a song, causing Zapdos to fall asleep.

"This is my chance!" Fluttershy says as she reaches into her backpack and pulls out an Ultra Ball. She throws the ball at Zapdos, which opens upon contact as a ray of red light emerges fro the ball and engulfs Zapdos before it disappears into the Ultra Ball. Once the ball hits the ground, it shakes back and forth three times before the a star emerges from the ball, signifying that Zapdos was caught. Fluttershy walks forward and picks up the ball as Piplup becomes engulfed in a bright light. Once the light dissipates, Fluttershy can see that Piplup had evolved into a Prinplup. Fluttershy returns Jigglypuff and Prinplup to their Pokeballs before she puts the balls into her backpack and turns to exit the power plant.

'One down, two to go.' Fluttershy thinks as she exits the plant and hops onto her bike.

Canterlot Skating Rink (Vs. Articuno)

Author's Note

Credit goes to lunarderpy1 for the idea of putting Articuno in a skating rink.

Canterlot Skating Rink (Vs. Articuno)

'So, this is where Articuno is.' Fluttershy thinks as her bike rolls to a stop in front of the indoor skating rink she used to go to when she was younger. She gets off of her bike and chains it to a bike rack located by the front door. She's about to go inside when she notices that people are walking away from the skating rink. She walks over to the door and sees a note posted on the door.

"I'm sorry to say that the skating rink is closed. Our cooling system went haywire last night, freezing the lobby." Fluttershy says, reading the note. "Sorry for any inconvenience this may have caused. Local Management"

Fluttershy, knowing that she has to get inside someway or another reaches for the handle to open the door. She pulls on the door, surprised to find it unlocked, and heads inside. The moment she does, she slips and falls.

"They w-weren't k-kidding." Fluttershy says, shivering as she attempts to stand back up. Once she does she notices that the lobby floor has been encased in ice. She attempts to take a step forward, only to slide until she collides painfully with the plastic doorway that separated the ice rink from the lobby. Fluttershy, after making sure she's alright, opens the door and steps inside to see Articuno at the center of the rink. Once she steps onto the ice, she slides forward until she collides with a pillar of ice, causing her to fall down.

"Ow!" Fluttershy exclaims as she uses the pillar to help her stand up. "Every t-time I take a s-step, I slide f-forward until something g-gets in my w-way." Fluttershy looks to her right and sees a pillar of ice a distance away from Articuno. Fluttershy looks to her left and sees the wall of the skating rink.

"Looks -llike I'm going r-right." Fluttershy says as she turns and takes a step, bracing herself for the impact. After colliding with the ice, she checks her surroundings and notices an ice pillar that will stop her in just the right place to let her slide to Articuno. She steps towards the pillar and collides with it a few moments later.

"H-here goes n-nothing," Fluttershy says, her teeth chattering, before she takes a step towards Articuno. She collides with smacks int Articuno a few seconds later and falls down as Articuno turns around and screeches at her.

"Articuno!" It screeches as Fluttershy reaches into her backpack and pulls out a Pokeball, preparing for battle.

"You can do it, Pikachu!" Fluttershy yells as she throws the Pokeball which opens in midair, letting the little yellow mouse out.

"PIKA!" Pikachu yells as it uses Thunderbolt, causing a large bolt of lightning to strike Articuno, as Articuno unleashes Blizzard, causing an onslaught of freezing snow to forcefully pelt Pikachu. Unfortunately, due to the cold conditions, Pikachu emerges from the attack frozen solid in a block of ice.

"You did your best, Pikachu." Fluttershy says as she returns Pikachu to its Pokeball. "Get warm, buddy." Fluttershy says as she puts the Pokeball in her backpack and pulls out another Pokeball.

"Give it your all, Prinplup!" Fluttershy yells as she lets Prinplup out of its Pokeball. Upon touching the ground, Prinplup lets loose Hydro Pump, which hits Articuno forcefully in the chest, knocking it back as Articuno retaliates with Ice Beam. Prinplup takes the hit, which knock it into the wall of the skating rink. Prinplup falls to the ground.

"Prinplup, come back!" Fluttershy says as she returns Prinplup to its Pokeball. She reaches into her backpack and pulls out another Pokeball.

"Go, Jigglypuff!" Fluttershy yells as she throws out the Pokeball, expecting the pink Balloon Pokemon to come out of the ball. However, a human sized red dragon with a flame on its tail pops out of the ball.

"Charizard!" It yells as Fluttershy stares at the creature, frightened, as Charizard engulfs itself in flames and flies at Articuno at maximum speed, catching Articuno off guard. Charizad strikes Articuno and a massive explosion occurs, burning Articuno and knocking Charizard away as Articuno slumps to the ground. Charizard turns and looks happily at the shivering Fluttershy, only to see the look of horror on Fluttershy's face. Charizard flies over to her as Fluttershy attempts to step back, only to slip on the ice. However, Fluttershy didn't hit the ground, having been caught by Charizard, who lands and envelops her in its warm wings. Charizard turns and places Fluttershy on the ground before it opens its mouth and uses Heat Wave in an attempt to warm the building. Eventually the lobby of the skating rink has thawed and Fluttershy is no longer freezing, which causes Fluttershy to look to Charizard, a look of surprise etched on her face as Charizrd flies over to her and nuzzles her hand.

'I-I think it wants my approval.'' Fluttershy thinks, realizing that Charizard warmed up the skating rink for her as Charizard brings her backpack to her.

"Char!" Charizard says as it tilts its head towards Articuno. Fluttershy reaches into her backpack and pulls out an Ultra Ball, which she lobs at Articuno. The ball opens, sucking Articuno into it, before it falls to the ground. It shakes a few times before a star emerges from the ball, signifying that Articuno had been caught. Fluttershy moves to grab the ball, but Charizard puts an arm out to stop her before it flew over to he ball and picked it up. Charizard flew back over to Fluttershy and put the ball in Fluttershy's hand. An awkward moment of silence passes before Fluttershy, looking uncertain, speaks up.

"Thank you." Fluttershy says as she pets Charizard on the head, which makes Charizard let out a content sigh.

"Fluttershy moves to return Charizard to its Pokeball, but before she can, Charizard suddenly flies at her and picks her up in its claws, causing Fluttershy to let out a small "Meep!" Charizard flies over to the doorway and gently puts Fluttershy on her feet.

"Thank you." Fluttershy says as she returns Charizard to its Pokeball. After doing that, Fluttershy puts both Charizard's Pokeball and Articuno's Ultra Ball into her backpack before she leaves the skating rink. She walks over to her bike, unlocks it, and hops on, noticing a bracelet on her arm the exact same arm that Charizard had nuzzled. Fluttershy ponders why Charizard would give her a bracelet as she kicks off, knowing that Moltres is all that remains before she can fight Mewtwo.

Everfree Forest (Vs. Moltres)

Author's Note

Legend of Everfree spoilers ahead. Read at your own risk.

Everfree Forest (Vs. Moltres)

Rainbow Dash had never been one to rise early in the morning. Sometimes, during school breaks, she wouldn't even get up before noon. So it was no surprise that Rainbow was woken at 11 AM by someone knocking on her front door. Rainbow slowly got out of bed and walked out of her bedroom before heading down the stairs. She stops at the front door, mumbling as the person knocks on her door again.

"I'm coming, hold your horses!" Rainbow snaps as she opens the door and sees Fluttershy standing on the front porch. Upon seeing Fluttershy, Rainbow's mood changes. "Hey, Fluttershy. What's up?"

"I'm on a quest, Rainbow! I have to catch the Legendary Birds." Fluttershy says as she releases Articuno and Zapdos from their Ultra Balls.

Rainbow stares at them, stunned for a moment before asking Fluttershy "So why are you here?"

"I was wondering if you could drive me somewhere," Futtershy says to her friend. "Moltres is located in the Everfree Forest, and its too far away for me to bike there."

"Why don't you just let your Charizard fly you there?"

"Because Charizard still scares me a little bit." Fluttershy replies honestly.

"Okay, let me get dressed and I'll drive you there." Rainbow sighs and heads back upstairs as Fluttershy returns Articuno and Zapdos.

An hour later, Rainbow pulls into the parking lot for Camp Everfree. Fluttershy and Rainbow exit the car and walk towards the trail that will take them into the forest. As soon as Fluttershy steps into the foliage, a piece of paper falls down from one of the trees and lands on her shoulder, startling the shy girl.

Rainbow reaches down and picks up the piece of paper before walking forward and placing a comforting hand on Fluttershy's shoulder.

"Relax, Fluttershy, it was just a piece of paper." Rainbow says as Fluttershy takes the piece of paper and reads it.

"You'll find Moltres at the end of the trail. Prepare your team for a hectic battle!

-Mewtwo"

Fluttershy looks at Rainbow as they start walking along the path. They see many exotic plants as they walk, including some remaining vines from when Gloriosa had become Gaia Everfree. It doesn't take them long to reach the end of the path where Fluttershy and Rainbow can see Moltres roosting in a tree. Fluttershy walks up to the tree, before turning to Rainbow.

"Well, we found Moltres," Fluttershy says as she walks back to Rainbow. "Now all we need to do is find a way to get it out of the tree."

"Why don't you try using Charizard?" Rainbow suggests as Fluttershy pulls a Pokeball from her backpack.

"Because I'm still not very comfortable around it," Fluttershy says as she throws the Pokeball, releasing Prinplup who emerges engulfed in a bright land. Upon landing, the bright light diffuses, revealing that Prinplup had evolved into an Empoleon.

"Empoleon, attack the tree!" Fluttershy commands. Empoleon rushes forward and headbutts the tree, which causes Moltres to fall to the ground, waking up in the process. Moltres lands and attacks by engulfing itself in a harsh light. Empoleon attacks with Bubblebeam, sending a stream of bubbles at Moltres which pop upon touching it. Moltres then attacks by unleashing Sky Attack, which makes it charge into the Empoleon with powerful wings of light. Empoleon runs forward and uses Drill Peck spiraling into Moltres as it pecks its beak into Moltres. Moltres uses the opportunity to absorb the surrounding sunlight. As Empoleon jumps back, Moltress unleashes Solar Beam, which knocks Empoleon over to Fluttershy's feet where it lays unconscious at her feet.

"You did great, Empoleon!" Fluttershy says as she returns Empoleon to its Pokeball. She reaches into her backpack to pull out another Pokeball when her hand feels a piece of paper. She pulls it out and reads it as she reaches for Pikachu's Pokeball.

'I hope you received my gift. Ness mentioned that you have a Charizard, so I think you can use this gift. Next time you send out Charizard, it should have a bracelet with it. Put it on your arm. I gave Ness a special object that will react with the stone in that bracelet. He should have hopefully given it to your Charizard. To get it to work, place your finger on the stone in the bracelet.

-Calem'

Fluttershy stops reaching for Pikachu's Pokeball as she hands the paper to Rainbow and starts to reach for a different Pokeball.

"Go get 'em, Charizard!" Fluttershy says as she throws the ball, unleashing the giant fire-breathing lizard the ball contained.

"Charizard!" Charizard yells as it looks expectantly at Fluttershy.

"Here goes nothing!" Fluttershy says as she touches the stone in her bracelet. Upon touching the stone, the bracelet becomes engulfed in purple light and four rays of purple light emerge from both the stone and Charizard. The purple light slowly forms a purplish sphere that surrounds Charizard. After a few moments, Charizard shatters through the sphere looking slightly different than it had before. It looked sleeker, more aerodynamic than it had before. In addition, there were several additional features. Protruding from the top of its head was another significantly larger horn. Protruding from its arms was another smaller set of wings. Protruding from its tail were three small spikes. As Charizard looks back at Fluttershy triumphantly, Rainbow Dash says what Fluttershy realized.

"Mega Charizard Y!"

Charizard looks up at the bright sunlight that showed up after it Mega Evolved before it quickly flies forward and unleashes a large ball of fire that reaches Moltres before it explodes violently, knocking Moltres back into the tree it had previously been sleeping in, breaking it before it falls to the ground.

Fluttershy reached into bag and pulled out an Ultra Ball as an exhausted Charizard walked back over to Fluttershy. Charizard waits for Fluttershy to throw the ball before it nuzzles her. Fluttershy gently pats it as she gets up and walks over to pick up the Ultra Ball, only to turn around and see that Charizard followed her all the way there.

"Great job, Charizard," Fluttershy says as she embraces the giant lizard before she returns it to its Pokeball and puts it and the Ultra Ball into her backpack.

Afraid of Shadows (Vs. ???)

Author's Note

Did you really think it would be that easy for Fluttershy?

Afraid of Shadows (Vs. ???)

Fluttershy looks around as Rainbow helps her up. She eventually notices a tree with a piece of paper attached to it. She walks over and removes the piece of paper. Fluttershy walks back to Rainbow and silently reads the note.

'I'm impressed. Now come find me. I'm in the Crystal Cave.

-Mewtwo'

Fluttershy looks at Rainbow Dash. "So it looks like we need to head to the Crystal Cave."

Rainbow starts walking back to the Camp. "Follow me. I remember where it is."

It about an hour for the girls to make it to the Crystal Cave. When the girls begin to see the entrance, they notice that a teenage boy wearing a red hat and shirt, blue full length jeans, red shoes and a yellow backpack is standing in the road. As Fluttershy gets closer, she notices that the teenager has a purplish shadowy aura surrounding him.

"Hey, kid! We'd like to get past." Rainbow says when they arrive at the entrance.

"Did you really think it would be that easy?"

Fluttershy cringes as she hears the demonic sounding voice coming from the kid.

"Did you really think I wouldn't have a final test for you?" The kid asks as he pulls a Pokeball out of his pocket and lets go of it. Fluttershy gasps as the Pokeball starts floating, suspended in the same shadowy aura. "In order to face me, you must face Red, the strongest Pokemon Trainer around!" Red says as the Pokeball that was being levitated suddenly opens, releasing a Blastoise.

"Looks like I've got no choice!" Fluttershy says as she pulls out a Pokeball. "Do it, Pikachu!" Fluttershy throws the ball, unleashing the little yellow mouse, who uses Thunder. Blastoise gets hit by the massive lightning bolt and retaliates with Hydro Pump. Pikachu gets knocked back before running at full speed. It engulfs itself with electricity before it collides with Blastoise. Pikachu bounces off as Blastoise falls backward, defeated.

Red returns Blastoise and sends out his next Pokemon, a Snorlax. Pikachu immediately attacks it with Thunderbolt. The attack appears to do little damage as Snorlax uses Giga Impact. Pikachu gets knocked back and lands at Fluttershy's feet. Pikachu attempts to get back up, only to slump down, unconscious.

"Good job, Pikachu." Fluttershy says as she returns the little electric mouse. She pulls out another Pokeball and lobs it, unleashing Jigglypuff who uses Hyper Voice, which causes a powerful sound wave to echo across the area. Snorlax doesn't move so Jigglypuff follows up with Double Edge, recklessly tackling its foe. After landing the blow, Snorlax slumps over and Red returns Snorlax before he sends out a Venusaur, which attacks with Giga Drain. Jigglypuff, who was already suffering from Double Edge's recoil, starts to tense up as its life force is absorbed by Venusaur. Eventually, Jigglypuff slumps down to the ground.

"Amazing job, Jigglypuff!" Fluttershy says, returning Jigglypuff before she sends out Empoleon, who uses Drill Peck while Venusaur returns with Frenzy Plant. Empoleon's peck connects at the same moment that it gets forcefully hit by a giant tree. Empoleon flies through the air and lands on its feet as Venusaur starts to regain its energy. Empoleon takes the opportunity to unleash another Drill Peck, which defeats Venusaur. Red returns the Pokemon and sends out his next Pokemon, a Charizard. The Charizard immediately uses Dragon Pulse upon leaving the ball. Empoleon gets launched backwards by the powerful shock wave. Fluttershy decides to return the penguin and send out her fourth Pokemon.

"Go Charizard!" Fluttershy yells as she throws the Pokeball opens letting the powerful dragon onto the battlefield. The two Charizard circle around one another before Fluttershy's uses Inferno. A massive stream of flames engulf Red's Charizard, which deals a moderate amount of damage. Red's Charizard attacks with Air Slash. The attack missed, and the blade of air would have hit Fluttershy, if it weren't for a set of claws snatching her up. Her Charizard tosses her onto its back and looks at the bracelet. Fluttershy nods and touches the stone embeded in it. Her Charizard immediately gets surrounded by the same purple energy that engulfed it in the battle against Moltres. The sphere shatters, unveiling Charizard's Mega Evolution. Fluttershy's Charizard looks at the other Charizard, and looking rather smug, builds up a bright white light in its mouth before it unleashes a powerful Hyper Beam at the opposing Charizard. The beam hits, knocking the opponent out of the sky, which hits the ground and slowly attempts to get back up before slumping into unconsciousness. Red was about to reach for another Pokeball before the same demonic voice speaks.

"That's enough! I'll see you inside." The voice says as the aura slowly dissipates and Red collapses to the ground.

Mewtwo Strikes Back (Vs. Mewtwo)

Fluttershy walks forward and attempts to enter the cave. She is stopped by Red slowly standing up and approaching her.

"Thank you for freeing me from Mewtwo's control." Red says as he reaches into his backpack. "Before you fight Mewtwo, I'd like to help prepare you're team." Red pulls out a yellow orb and some Potions and Revives. "If you'll let your Pokemon out, I'll heal them for you."

Fluttershy reaches into her backpack and pulls out her Pokeballs, letting her Pokemon out. Red gets to work reviving her fainted Pokemon as Fluttershy looks at the orb. Red finishes with Empoleon and Jigglypuff before turning to work on Pikachu, grabbing the orb in the process. "This orb is a Light Ball. It's a special item that only works on Pikachu." He says as he gives the orb to Pikachu to hold. "It increases a Pikachu's Attack and Special Attack." He says as he uses a Hyper Potion on Pikachu, instantly making it perk up. After finishing with Pikachu, Red moves onto Charizard and quickly sprays a Max Potion over it, fully healing the Pokemon.

"There. Now you should be good to go." Red says as he places the used items in a special pocket of his bag and stands up. Fluttershy returns her Pokemon and enters the cave with Red and Rainbow to find Mewtwo standing in front of the panel where Gloriosa had found the magical geodes. Mewtwo turns around and looks at Fluttershy with contempt in its eyes.

"Hmm. You are stronger than I expected." Fluttershy and the others hear as Mewtwo speaks to their minds. "I will allow you to battle me. Prepare to lose!"

Fluttershy takes off her backpack and opens it to reach for one of the Legendary Birds when the three Ultra Balls suddenly float out on there own as Mewtwo's voice reaches Fluttershy's mind again.

"I can't let you use those beings!" The voice says fearfully as the balls start to shake before unleashing their contents. The three birds flock together above the center of the arena as the ground starts to shake. Suddenly, a ring appears before Fluttershy and a white and blue bird Pokemon emerges from the ring.

"LUGIA!" The bird screeches as it looks up at the trio it reigns over, who nod at Fluttershy. Luiga looks back at her before it launches an Aeroblast at Mewtwo, causing a vortex of air to hit Mewtwo as Mewtwo looks on in fear for a moment before attacking with Psystrike, unleashing a severe jolt of telekinetic energy upon Lugia as Lugia suddenly causes time to temporarily stand still. After time starts back up, Mewtwo attacks by building up an orb of blue energy before it throws an Aura Sphere at Lugia. Luigi returns suit by engulfing itself in a bright light while Mewtwo attacks by launching a ball of pure shadow at Lugia. This knocks Lugia back as it unleashes the light in the form of Sky Attack, causes wings of light to collide with Mewtwo as Lugia collapses from the Shadow Ball.

"You can do it, Charizard!" Fluttershy yells as she throws out a Pokeball and the fire-flying lizard appears on the battlefield. Charizard looks back as Fluttershy touches the stone in her bracelet, which causes Charizard to Mega Evolve. As a bright sunshine appears in the cave, Charizard attacks with Inferno. This caused massive flames to erupt from Charizard's mouth and engulf Mewtwo, burning it. Mewtwo then suddenly stops in time as it receives a sudden psychokinetic jolt from Lugia's Future Sight. Mewtwo drops to one knee as Charizard uses Heat Wave to defeat Mewtwo.

"We-we did it!" Fluttershy says as she rushes forward and embraces Charizard before she walks back over to her backpack and pulls out an Pokeball and lobs it at Mewtwo, who enters the ball. A star emerges from the ball as soon as it hits the ground. As Fluttershy moves to puts the Pokeball into her backpack, she notices that the Legendary Birds are surrounding her. The birds start to speak to her.

"Zapdos!" ("We knew what Mewtwo had been up to.")

"Moltres!" ("And we knew that it would take a fellow Legend's help to beat him.")

"Articuno!" ("So when Mewtwo tried to remove us, we knew we had to bring master Lugia to help you.")

"Zap!" (Use a Pokeball and capture our leader. It will allow Lugia to survive this ordeal.")

The three birds let out a final screech that Fluttershy understood to mean "Please save our master." She reahes into her bag, pulls out a Pokeball and throws it at Lugia. As soon as the ball hits Lugia, it opens, drawing in the white bird before it closes and shakes in the air. The ball hits the ground and emits a star as Fluttershy walks over to it. She picks it up and puts it into her bag as the Legendary Birds land by her side, each one of them holding their respective Ultra Ball in their talons. They each drop their ball their owners feet and Fluttershy returns them before walking out of the cave with Rainbow and Red. Rainbow starts to walk with Red towards the campgrounds before she notices that Fluttershy is standing at the entrance to the cave with Charizard at her side.

"Fluttershy? You coming?" Rainbow asks Fluttershy as she sees Fluttershy climb onto Charizard's back.

"You go on ahead, Rainbow. I think I'll fly back." Fluttrshy says as Charizard starts to fly towards Fluttershy's house.

Author's Note

Thank you for reading my story. I really enjoy the way this story turned out. But it feels like something, or someone, is missing. So, like my previous stories, there will be a bonus scene in the works. I plan for it to feature the missing Kanto Legend. It probably won't be up until after Pokemon Sun and Moon come out.

Fluttershy and the Mystery of Mew (Bonus Scene)

It had been a week wince Fluttershy had went on her quest when she woke up to an odd sight. There was someone who looked distinctly like her standing to the side of her bed. Fluttershy nearly screamed upon seeing herself before she remembered hearing from Sunset that there was another Fluttershy in the world that Princess Twilight called home. Thinking that this was her other self, she got out of bed and slowly approached before offering her hand.

"U-um, hello? My n-name's Fluttershy." Fluttershy says as the other Fluttershy slowly moves her hand forward and grips her hand.

"MEW!" "Fluttershy" says as she starts to change. It takes less than a few seconds for "her" to turn into a floating creature that resembled a pink catlike creature. Fluttershy looks confused at the Mew before she remembers that Mew can use Transform, allowing it to take the form of any living thing it wants. However, this confuses Fluttershy even more. Why would Mew want to take her form.

"Mew!" Mew says smiling at the confounded look on Fluttershy's face before flying in a loop around Fluttershy. It then notices the Pokeballs on her bedside table, sensing that there is something familiar in one of the balls.

"Mew!" Mew yells at one of the Pokeballs as Fluttershy walks over and examines the ball, realizing that Mew's clone is in the ball. Fluttershy remembers that Mewtwo once had an intense rivalry with the creature that it was created from.

"You recognize Mewtwo?" Fluttershy asks Mew. Mew nods and does a playful flip in the air before flying back over to Fluttershy as someone knocks on her door. Upon hearing the knock, Mew appears startled and uses Transform making it look like a nervous Angel. Fluttershy smiles as she walks out of the room and opens ther front door to see her friends on the other side.

"Hey, girls. What's up."

"Pinkie was thinking of heading over to Sugar Cube Corner." Rainbow says as Pinkie jumps up and down. "You want to come?"

"Sure, just let me get changed real quick." Fluttershy says as she turns around and sees "Angel" standing there with a mischievous look on its face. "You play nice with my friends, okay?" Fluttershy says to the "bunny" as she leaves the room. Once she enters her bedroom, and closes the door, she pulls out the shirt she wore to Camp Everfree and a green denim skirt. It only took her a few minutes to get dressed. However, once she returns to the living room, she sees that there is a confused look on everyone's face, except for the second Twilight Sparkle who has a playful look in its eyes behind the glasses.

Fluttershy sighs and looks over at the other "Twilight". "Mew! I told you to play nice." The "Twilight" looks downtrodden as it transforms back into the pink catlike creature from before.

"Mew!" Mew exclaims as Pinkie gasps in shock.

"You found a MEW!" Pinkie says unable to believe the sight before her.

"How did you find this thing, sugar cube?" Applejack asks as she turns to look at Fluttershy.

"It was standing over my bed this morning." Fluttershy says, starting her explanation. "When I woke up, it was there, and it looked just like me. I thought it might have been the other Fluttershy from Equestria, so I went over and introduced myself. It surprised me when I saw it change before my eyes." Fluttershy says as Mew Transforms into Rainbow, then Sunset, before finally changing back into Fluttershy.

"It seems like the little fella has taken a liking to you." Rairty says as the group of seven girls see Mew use Fluttershy's form to walk over to the shy girl.

"I guess you can say that I now know how our Twilight felt when she first met Princess Twilight." Fluttershy says as Mew jumps and Transforms back into its catlike form before nuzzling her. Mew then lands, sitting on the ground expectantly as Fluttershy and the girls move to leave the house. However, before Fluttershy can step over the threshold, she feels something pulling on her arm. She looks back and sees Mew there clinging to her arm.

"I take it you want to come with me?" Fluttershy asks Mew. Mew lets go and nods vigorously before flipping in joy. "Okay, you can come along, but we'll have to do something about your appearance.

"Mew!" Mew says as it Transforms into a perfect duplicate of Fluttershy.

"Um, maybe we should try something else," Fluttershy says as she walks back into her house to look for a photograph.

An hour later the seven girls enter Sugar Cube Corner alongside someone who looks like Fluttershy's brother, Zephyr Breeze. The group of eight quickly find a table and sit down while Pinkie gets in line to place their orders. Fluttershy turns to look at her "brother".

"Remember, you are my brother, Zephyr, and you're not supposed to speak." Fluttershy says as "Zephyr" nods and whispers "Mew!" as Pinkie returns with some cupcakes and drinks. She places one in front of everyone, except for "Zephyr" who gets a small brown spherical cake.

"I hope Zephyr likes his cake." Pinkie says before she whispers "I had Mrs. Cake make something akin to a Pokepuff for him." Pinkie says as "Zephyr" picks the cake up and tentatively takes a bite. It didn't take long for "him" to finish the pastry.

The girls sit and talk for a while. The entire time, Fluttershy looks concerned between the other patrons and "Zephyr".

"You have no reason to fret, darling." Rarity says to Fluttershy, trying to reassure her. "No one knows that 'Zephyr' here is actually a creature from another universe." Rarity says before she takes a sip of her drink. "And no one will ever know as long as 'he' doesn't talk or-" Rarity is cut off as the group notices someone enter the cafe.

"Or Zephyr enters the building." Rarity finishes her previous statement as Fluttershy's brother walks through the door, a bell chiming ass the door closes behind him.

"Get under the table!" Flutershy whispers to Mew as Zephyr gets in line. Zephyr notices the group just as Mew has gotten situated under the table, with the tablecloth obstructing Zephyr from seeing it. After Zephyr places his order he goes over to Fluttershy's table.

"Hey, sis!" Zephyr says before turning to Rainbow. "Rainbow Dash. What are you two doing here."

Fluttershy was about to answer, but was beaten to the punch by Rainbow.

"We're having a pleasant time by ourselves, Zephyr." Rainbow says a little harshly. "So could please go find somewhere else to sit?"

"Okay, just let me get my order and I'll be out of your hair." Zephyr says as he hears Mrs. Cake call his name. He walks over to the counter, picks up his order, and leaves the cafe.

"You can come out now," Fluttershy says as she leans under the table and helps "Zephyr" get back into "his" seat. "Zephyr" runs his hand over his forehead, relieved that he wasn't caught.

"That was close," Rainbow says as the group resumes their previous conversations while they slowly work on their cakes.

An hour later, Fluttershy is back home with Mew in her room. Mew flies over to her backpack and pulls out a Pokeball before flying back over and nuzzling Fluttershy's hand. Mew drops the ball at her feet and performs a little flip as Fluttershy realizes what it wants. She reaches down and picks up the ball as Mew lands on the ground, waiting for Fluttershy to throw the ball. Once she does, Mew jumps up and collides with the ball. The ball opens and Mew goes inside. Once the ball closes, it falls to the ground and a star emerges.

"Welcome home, Mew." Fluttershy says as she picks up the ball and puts it on the bedside table with the rest of her Pokemon's Pokeballs.

Author's Note

As promised, here is the bonus scene featuring the missing Legend (I know Mew is now technically called a Mythical Pokemon, but I'm old school, so Mew will always be a Legenadary Pokemon to me). I might decide to make a sequel, but that will have to wait until after I have played Pokemon Sun and Moon. That way I'd have some extra scenarios to work with, as well as ~100 more Pokemon that I could sick upon Fluttershy.

Ruler of Nightmares (Bonus Scene 2)

Author's Note

I seriously didn't consider making a second bonus scene, but I recently had theinteresting idea of having Fluttershy terrorized by the Pokemon of Nightmares.

Ruler of Nightmares (Bonus Scene 2)

Fluttershy slowly opens her eyes. She notices that she appears to be on a large island wearing her usual clothing with her backpack on her back. She finds this odd. The last thing she could remember doing was getting in bed. And now suddenly she appears to be stuck on a large island with a giant demonic version of Angel Bunny.

'Wait, that wasn't there before.' Fluttershy thinks as the bunny slowly starts to walk towards her with a demented smile on its face. Fluttershy turns and runs for the trees at the edge of the clearing as the bunny laughs. She makes it into the treeline just as she hears the rabbit start crashing through the trees, snapping them like they're twigs. Upon hearing that, Fluttershy picks up the pace running like she's never run before. Along the way, she sees a dark black creature in a clearing off to her left. Upon hearing the giant rabbit crashing through the trees diagonally to the right behind her, she decides to take her chances with the dark creature to her right. She sharply turns and runs at top speed, entering the clearing as she hears the rabbit close behind her. She runs to the center of the clearing and turns around expecting to see the rabbit coming for her. However, as she looks back, she notices that the bunny has disappeared.

'What? Where'd it go' Fluttershy thinks as gasps for breath. She soon hears a noise from behind her. She turns around expecting to see the rabbit, only to see the pitch black creature from before. Flutershy glares as it appears to be laughing at her. It slowly stops and stares at her as Fluttershy reaches into her backpack and pulls out a Pokeball. She was about to throw it when the dark creature shrieks, suddenly making it appear like it engulfed the entire island into the darkest of nights. The creature laughs at the shocked look on Fluttershy's face before Fluttershy calms down and attempts to throw the ball, only to feel something fall onto shoulder. Fluttershy screams out as it slowly slips off and falls to the ground in front of her. She looks down, her heart going a mile a minute, as notices that it looks like a glowing green feather shaped like a crescent moon. She reaches down and picks it up.

'A Lunar Wing?' Fluttershy thinks, recognizing the general design of the item. 'But that must mean that,' She thinks as she looks left, then right, then slowly looks up, where she sees the Legendary Cresselia, who illuminates the area surrounding her, comforting Fluttershy.

'Wait, is this a dream?' Fluttershy thinks as it dawns on her. 'Then that must mean . . . ' Fluttershy thinks as she tightens her grip on the Pokeball in her hand before she lobs the ball, unleashing her Charizard. Immediately, Charizard glares at the dark pokemon as Fluttershy reaches for her bracelet, only to realize that it's not on her arm.

'Where'd he Mega Bracelet go?' She thinks as she hears the creature snicker. Charizard looks back at its master, concerned for her, before it attacks Darkrai with Heat Wave, heating up the entire area and setting the trees on fire. Darkrai appears to laugh before Charizard gets sucked into a dark void at its feet. CHarizard soon reappears, fast asleep, as it appears to be cringing in pain. Darkrai laughs as a cloud emerges from Charizard, which shows its dreams, and slowly floats over to Darkrai, who eats it. Fluttershy looks on as Charizard suffers before she returns it and sends out Jigglypuff who uses Dazzling Gleam, which causes a powerful flash to illuminate the area and causes Darkrai to cringe in severe pain. Darkrai attempts to drag Jigglypuff into a Dark Void, but Jigglypuff leaps and floats to the side of the void before Jigglypuff sings, lulling Darkrai to sleep. Fluttershy reaches into her bag and pulls out an Ultra Ball which lobs at Darkrai. The ball makes a whooshing sound as it flies through the air before it hits Darkrai, dragging the Pokemon into the ball. The ball shakes in midair after it closes. It hits the ground and shakes once before a star emerges, signifying that Darkrai had been caught. Flutershy walks forward and picks up the ball as a voice appears in her mind.

"Thank you for taking care of Darkrai." Fluttershy realizes that it was Cresselia who was speaking to her. "Darkrai's been terrorizing people's dreas for the last few days. Thanks to you, people can sleep peacefully from now on." Cresselia says to Fluttershy's mind as the environment surrounding her starts to fade until only Fluttershy and Cresselia are left floating in a white void. "It's time for you to wake up, but I think we'll meet again soon." Cresselia says as it fades from Fluttershy's sight and and her eyes start to feel heavy. She closes her eyes and opens them waking up in her bed with an Ultra Ball and a Pokeball on top of her bedsheets.

'Was it a dream?' Fluttershy thinks as she hears a voice in her head.

"It was a dream. But what happened in the dream really did happen." Cresselia voice tells Fluttershy, explaining what was in the Ultra Ball. "I wanted to thank you personally for helping, so I decided to join your team." The voice says explaining the Pokeball on the bed. "Feel free to use me in battle. I will help you to the fullest of my ability." Cresselia finishes as the Lunar Wing Fluttershy's dream slowly floats down onto Cresselia's Pokeball.

Pokemon Contest Spectacular! (Bonus Scene 3)

Author's Note

Another Bonus Scene for your enjoyment! Fluttershy has taken on one of the strongest Pokemon of all time and defeated the strongest Trainer in the multiverse. Now she has to deal with one of her worst fears. Being the center of attention.

Pokemon Contest Spectacular! (Bonus Scene 3)

"Rarity, I really don't want to do this." A voice says from behind the changing room door.

"You've got nothing to worry about, darling. When I found out you had a Pikachu, I knew I just had to try out some new designs."

The door opens slightly and Fluttershy emerges with Pikachu. The two were wearing matching pink and white two piece costumes that a pop star would have worn. A bracelet containing Fluttershy's Key Stone in a heart-shaped charm adorned her left arm.

"Rarity, it's not modeling the costumes that worries me." Fluttershy says as she strides over to Rarity. "What worries me is that you're wanting me to wear this in the Pokemon Super Contest Spectacular here in the Slateport Pokemon Contest Hall!"

"So?" Rarity asks innocently.

"I really don't want to participate in the Pokemon Contest."

"Fluttershy, Rainbow told me that you took on the strongest Pokemon Trainer of all time and captured a Pokemon that once wanted to eradicate all mankind. You're seriously telling me that a little Contest frightens you?" Rarity asks skeptically as a woman dressed in a similar two piece blue and white outfit enters the dressing room with an Altaria following behind her.

"Oh don't mind me," The woman says as Rarity and Fluttershy turn to look at her. "I'm just waiting here for one of my proteges. His contest should be ending soon." She says as she walks over towards one side of the room. A couple of teenagers, a boy and a girl, enter the room a moment later hand in hand. The boy was dressed in a red jacket and shoes with black pants and a black shirt with yellow accents on it, while the girl was wearing a red tank top over a black tank top with a pair of white shorts over her black biker shorts. A red headband with a bow on it adorned her hair and a yellow and green fanny pack was around her waist. A pair of yellow shoes were on her feet.

"Hey, Lisia. You wanted to see me?" The boy asks as he and the girl walk over to Lisia.

"Yeah, I wanted to congratulate you on your victory, Brendan." Lisia says as she walks extravagantly over to Brendan before she notices the girl next to him. "And I wanted to wish you luck in the next Contest, May." She says as Rarity and Fluttershy look at one another, concern on their faces.

"Does this mean I'll have to face her?" Fluttershy whispers to Rarity as they leave the dressing room and head for the registration desk.

"Without a doubt, darling." Rarity says as Fluttershy sighs.

-One Cuteness Contest Later-

Fluttershy emerges from the stage doors with a sad look on her face. Even though she and her Pikachu had given it their all, the duo had lost to May and her Audino. The two had been neck and neck until May's Audino Mega Evolved. Feeling dejected, Fluttershy wanted to get out of the Contest Hall as fast as possible. However, upon reaching the other side of the registration desk, the receptionist stopped her before she could flee the establishment.

"Oh, Miss Fluttershy? Someone seems to be waiting for you in the dressing room."

'Great, now I have to face Rarity,' Fluttershy thought as she starts to walk towards the dressing room.

"You wanted to see me, Rarity?" Fluttershy asks as she enters the room, only to see that Rarity is not in the room. Waiting in the center of the room is Lisia and Brendan.

"Where's Rarity? I had been told that she wanted to see me." Fluttershy says to the duo as May enters the room in an outfit nearly identical to Fluttershy's. Lisia turns to May, and starts whispering to her. A smile slowly spreads upon May's face before she turns to Fluttershy.

"I wanted to congratulate, Fluttershy." May says as she offers the hand of fellowship.

Fluttershy looks at May confused as she shakes her hand. "But I lost."

"Yeah, but you gave me a run for my money." May says as Lisia steps forward. "Like Lisia, I can see that you have potential as a contest coordinator, which is why we want to take you on as our apprentice." May says as Fluttershy starts to hear Rarity's voice coming from the doorway.

"Can I talk to Rarity about it?" Fluttershy asks as Rarity enters the room.

"Talk to me about what?" Rarity asks.

"They want to take me on as their apprentice." Fluttershy says. Rarity pulls Fluttershy aside and confer with one another quietly. Eventually, Fluttershy turns back to May.

"I'm in," Fluttershy says, shaking hands with Lisia, sealing the arrangement.

Welcome to the World of Ponymon!

"Uh, I-I'll also take a few Hyper Potions, and a couple dozen Ultra Balls, if that's alright with you."

The clerk grabs the desired items and puts them on the counter in front of him. "That'll be 32,400 poke dollars."

Fluttershy reaches into her pocket and pulls out some of the money that Ness gave her when she stepped through the portal into his universe and hands it to the clerk. "Thank you." She says as she puts the items she just bought into her backpack and turns to leave, with a Pikachu following close behind her.

"You ready to go back home?" She asks the little yellow mouse as they walk towards the boat that would take them back to Onett.

"Pika!"

"Well, then lets go." She says as she pulls out Pikachu's Pokeball.

'What will I do with you?' She mentally asks the creature inside the Pokeball as she opens the door to her house and heads to her room. Inside of the ball is a Charizard, a Pokemon that frightens her to no end. "I want to be your friend, but . . . " She trails off as she notices a piece of paper on her bedside table. She picks it up and reads it.

'I heard that some Pokemon have been traveling over to this universe, most of them so because of you. I'm wondering what they see in you. So I'm offering you a challenge that I won't let you refuse. If you can form a team that will let you defeat the Legendary Birds, then I'll give you a chance to fight me.

-Mewtwo.'

Fluttershy sighs. "I'll start his challenge in the morning." She says as she gets ready for bed.

-That Night-

A pink creature used the pet door to sneak into the house. It only took it a matter of moments to find the pink haired girl sleeping in her bed. It hopped up onto her bed and went to sleep next to her, putting it's microphone and marker down next to it.

Author's Note

And so Fluttershy's adventure begins!