Goh and Raboot stood guard over Lumiose City jail. It was pretty quiet.
Until a blonde dude about Goh's age walked up to the office, crying. Goh worked up the courage to talk to him.
"Hi there, uh, what's wrong?"
The kid looked up at him through his round glasses, startled. He wiped the tears from his eyes.
"I'm sorry, I didn't see you there."
"So... why were you crying?"
"...My sister... she's gone missing."
Goh recalled that the man with the straw hat had said they were working on a missing person case.
"What does she look like?"
"Well," the blonde kid lifted his hand a little below his shoulder, "she's about this tall, is blonde with blue eyes like me, and she's almost always with a dedenne she carries around in a yellow satchel."
Goh noticed the blonde seemed really tired. His eyes were puffed and his hair was a mess. He wondered how long his sister had been missing, but didn't ask.
"I'll make sure to report it if I see her. What's her name?"
The blonde said her name like it was made of thin glass.
"Bonnie."
Goh and the dude held a moment of respectful silence for her.
Goh opened the door for him, assuring him that,
"I'll tell my friends Ash and Alain to keep a lookout too."
The blonde dude stopped short of the doorway.
"Ash? Alain?"
"You know them?!"
"Their partners are Pikachu and Charizard, correct?"
"Yeah-"
"Do you know where they are right now?"
"Yeah, on the other side of the building-"
The blonde dude rushed around the building, struggling to keep a heavy backpack from falling off his shoulders. Goh followed in pursuit.
"Raboot, stay here! We'll be back!"
When blonde dude and Goh turned the corner, they were shocked to find Alain on the ground, moaning and flailing about.
"Alain!" they both shouted.
Alain ripped off his scarf, revealing a small chip with a little red light strobing on his neck. The blonde rushed over and pulled a tiny screwdriver from his pocket. He unscrewed the top plate and briefly scrutinized the insides before deactivating the small device and taking it off.
The first thing Alain did after that was throw out Charizard's pokéball. He shakily took off the pokémon's chest plate to reveal another chip. The blonde dude removed that one too.
Alain quietly voiced his gratitude;
"Thank you, Clemont."
Then promptly fell limp into Charizard's arms.
Clemont felt his wrist and sighed in relief.
"He's asleep."
Goh panicked:
"Ash, Greninja, and Pikachu are gone?! And what happened to Alain?! We have to go find them!"
"You see these devices?"
Clemont held the two little metal squares up to Goh.
"These are mind-control chips. This is an organized crime. Probably the work of a group like Team Flare!"
"Ash and Alain were talking about their old boss being around-"
Clemont gasped.
"Lysandre?!"
"That's what they said!"
"We have to figure out some way to find Ash and the others! Maybe... they took Bonnie too."
Clemont and Goh both held their hands to their chins in serious thought. Goh spoke up,
"Ash has a phone!"
Goh took it out to call him-
"Wait!" Clemont stopped him.
"What?"
"If you call Ash, then we can trace his phone's signal back to wherever he is!"
"But how?"
Clemont did the anime glasses thing.
"The future is now, thanks to science!"(1)
Clemont pulled a small device out of his pocket.
"I thought we'd encounter a situation precisely like this one!"(2)
"What's that?"
"I'm glad you asked! This is the Rotom Tracker! Connect this to your phone and it will record the location of whoever you call!"
"Wow! That's great!"
The back door of the jail building burst open.
"Stop right there, ya fiends!"
"Huh?"
Goh and Clemont turned around to see the man with the straw hat with a few other police officers behind him.
"Gah- lee! They're gone!"
"Who?"
"Them dad-gum sunglass-wearin' scroundrels! They came right in an' took half the pris'ners out!"
Clemont was clearly surprised. Goh was skeptical.
"Why didn't you stop them?"
"I don't know. That didn't make any sense ta me either."
Goh and Clemont had an idea of what was going on. Clemont hesitated before asking the question:
"Um, sir, this may sound strange, but can I see your neck?"
"Y'all are senile."
"Please, sir."
"You ain't gon' lay a hand on me, son."
Clemont gave up.
"Team Flare must have planted the chips on the police officers as well."
"We have to do something about this!"
"I agree. Plug the Rotom Tracker into your phone and let's call Ash."
•.•.••.•.•
"You have a call from Goh.
"You have a call from Goh."
"Huh?" Ash heard the voice of Rotom from his pocket. The scruffy voice of a Team Neo Flare grunt scoffed:
"Heh, aren't ya gonna answer that, kid?"
Ash ignored the rhetorical question. His hands and feet as well as the appendages of the six pokémon with him (Glarian Farfetch'd, Dragonite, Gengar, Riolu, Pikachu, and Greninja) were locked inside metal spheres that spread them all flat against the walls of the van. This grunt in charge of watching them took sadistic pleasure in watching Ash cringe at the repeating ring of the call he couldn't answer.
"You have a call from Goh.
"You have a call from Goh."
Ash growled. The grunt laughed.
"You have a call from Goh.
"You have a call from Goh."
The ring ended and the voicemail kicked in.
"Hey, Ash. It's me; Goh. Hope you're doing okay. We're gonna find you; just hold on."
Beep!
"Your stupid friend won't find ya where you're goin'."
Ash grit his teeth at the grunt.
"Let us go."
"Actually, I take that back. You're friend is a genuis compared to you if ya think I'd just letcha go."
"Grrrr."
Ash and the pokémon voiced their displeasure. The Team Neo Flare Grunt folded his arms behind his head and smiled tauntingly at them.
The minutes dragged across the road with the van. Finally it came to a stop.
The van door opened, and the grunt took out a remote. He pointed it at the metal spheres and Ash & co. were floated outside to where Lysandre was waiting.
"Alright, got 'em, Lysandre."
"Good."
"Let doomsday begin!"
The last quote was from a voice that sounded... well, nothing describes Xerosic's voice better than... it sounds like a squid.
Ash & co were taken to the top of Lumiose Tower to hover high above the top ledge; a familiar veiw, and not in a good way. Xerosic stood next to a giant red laser canon, and the team grunts stood next to an even bigger green one.
"Thanks to the amazing power of Zygarde under our possession, I believe we can now summon the Red Shuriken!"
Ash had nothing better to do than to ask,
"What's that?"
"What's that, you ask? I'll tell you!"
Xerosic's squidly voice got all excited.
"As I'm sure you remember, in the Kalos League finals you and Greninja pulled off a stunning orange shuriken! After much research I've concluded this color was a result of the Zygarde cells under Team Flare's Control. I believe somehow the red vines the controlled cells made were connected with tinting the shuriken. So, I theorized, full possession of Zygarde would summon a Red Shuriken!"
"How'd you get control of both Zygarde?!"
"Another great question! We discovered the last time we tried to control Zygarde, our endeavors were stopped by a little girl named Bonnie. So we simply took her!"
"You wouldn't dare." Ash fumed.
"Ha! Yes I would!" Xerosic laughed.
"Now," Xerosic continued, "you may be wondering how I was able to do so much in jail! Well, even though Lysandre had to lay low and pretend to be dead for a while to escape Malva, once she turned herself in believing to have caught all the Team Flare members, Lysandre came out of hiding. He found my Team Neo Flare and... we used mind control chips to get into the police's heads!"
Ash didn't actually think into it that far, but now Alain's betrayal made so much more sense.
"You controlled Alain too!"
Lysandre explained this time.
"He came to save Greninja all on his own. Bad choice. But we let him off with a warning-"
"-And maybe a microchip!"
As Xerosic laughed some more, Lysandre explained the final parts of their glorious plan.
"We have all the power we need from Zygarde, and now, your Red Shuriken Ash-Greninja will be the final weapon!"
Lysandre motioned to the Team Flare/Neo Flare grunts standing by the ginormous green machine holding what can only be assumed as Zygarde 100% forme.
The grunts shot energy into the ground far below. Greninja flinched a split second before red-pulsed vines exploded from the dirt like mutant worms.
Lysandre then motioned to Xerosic.
Xerosic pointed the laser cannon at Ash and Greninja.
Ash had been through this moment a million times in forgotten nightmares.
A beam of red light overwhelming his senses.
A piercing ringing unlike any other.
"Pikapi!" a little voice called out.
He would get through it. They would get through it.
"Greninja!"
"Gren!"
Drip...
They were in a void with water all around.
Ash felt an out-of-body experience.
Greninja felt a connection with another spirit.
But something was wrong.
Ash went in to grab hold of Greninja...
"Turn off Bond Phenomenon."
Greninja slipped away, leaving Ash to lunge at nothing but air. He splashed face-down into the watery floor... and kept going.
"Mind control of Greninja is successful."
Ash plunged into a deep pool. He couldn't swim, he just kept sinking...
"Pending mind control on Ash."
He reached for something to hold, finding vast nothing.
"Turning on Greninja's implanted microchip's second function."
He tried to yell, nothing came out.
"Connecting to Vine Energy."
The water began to grow hot...
"Enhancing Bond Phenomenon to Red Shuriken Ash-Greninja."
Ash could feel the weight of pounds of water crushing down on him, and the heat of invisible flames scorching him from the inside out. He couldn't move, he couldn't breath, he couldn't scream-
"Mind control of Ash is successful."
He plunged upside-down into a flip-side world of red water. He didn't know where or when or how. But a torrent of angry red water surrounded him and Greninja.
"We have successfully completed the transformation of-"
And they emerged from the torrent as
"-Red Shuriken Ash-Greninja."
The steely bonds holding Ash and Greninja back were burst apart. Ash-Greninja floated down to the ledge of Lumiose Tower on a chariot of fire.
The red spikes on Ash-Greninja's head glowed bright red, and similar lights glowed in the eyes of Greninja and Ash. Above all, the hellish light of the Red Shuriken on Greninja's back throbbed in time to the dark music playing in their synced heartbeats.
Ash was no longer in his own head.
Heh, he wasn't even in control of his head.
Greninja felt the parasite of another blackened soul latch onto his own.
Rage.
Hate.
Chaos.
Ash-Greninja saw the vines writhing below in a new light. Now they were energy.
Now they were one.
Ash-Greninja raised their hands in the air. The vines rose with them. They strung the vines along like strings on a puppet entwined in their fingers.
"Stop right there, Lysandre!"
Opposition?
Ash-Greninja spun around, dropping the proverbial puppet. A face appeared, a familiar face. Two, in fact. But who they were didn't matter. They were standing in the way of a perfect new world.
"Ash! Greninja!"
Master Lysandre spoke:
"Prepare for the end of this world, and the beginnings of a far better one!"
His voiced dropped its coldness, and gained an otherworldly heat.
"Soon my dream of a more beautiful world will become a reality!"
Goh wouldn't have it.
"ASH!!! What's happened to you?!"
Clemont stood in shock for a moment, then he pulled something metallic out of his pocket. He rushed towards Ash-Greninja with it.
SQVROOOOMM!!!
A huge red vine sprang up out of nowhere and smashed Clemont.
Goh couldn't really believe it.
"Uh-h-h-..." his voice quavered. He looked towards his 'friend' in pure fear.
"Ah- Ash...?!"
Ash didn't reply. He gave Goh a mindless, glowing stare he'd never forget.
"Red Shuriken Ash-Greninja! Use Demolition Shuriken!
Ash abruptly yanked his gaze from Goh and began the process of fulfilling Lysandre's command.
Ash-Greninja summoned a squad of red tentacles. They weaved them into the Red Shuriken with their hands, spinning them into a beast of a throbbing red vine-blade that was growing bigger by the second.
Lysandre smiled at the sweet pandemonium.
"And now, for the rebirth of this world! Judgement will come to those who have misused it! Peace and beauty eternal for those who have saved it!
Ash-Greninja brandished the Ultimate Red Shuriken as a scythe to the death of the world.
"PIKAPI!!!"
And hesitated.
This was the same view. The same view from where they'd almost witnessed the end of the world. All those innocent people-
Did he squash Clemont just now?
"ARGH!"
Ash couldn't take it anymore.
The red vines writhed uncontrollably, some splitting the green laser cannon in half.
Zygarde 100% forme was freed.
Xerosic's squidly voice rose to a new pitch:
"Ash is losing his mind!"
Chaos reigned supreme. Greninja held the Red Shuriken to the sky with a shaking arm. Ash held his head in his hands and screamed. The memory of a dead friend haunted their hearts as red vines spasmed into uncontrollable contortions.
Goh tried something; Zygarde was free so-
"Zygarde! Please, use Power Construct!"
Zygarde fired at Lysandre-
and Ash-Greninja both jumped in the way.
"ASH!!! GRENINJA!!!"
The dust cleared and Ash-Greninja were seen lying on the ground.
Goh gasped.
A green spark flashed from the Red Shuriken.
"You're being li- like Lysandre."
Ash croaked out,
"Putting the life of someone into your own hands."
Lysandre was amazed. He was sure that Ash-Greninja weren't being controlled right then.
"But, he's-" Goh protested.
"I don't care what he's done."
Another green spark.
"Lysandre may be bad, but he deserves the chance to change."
Ash-Greninja stood up with a new light in their eyes. The Red Shuriken washed green. Ash shouted,
"The Healing Hand of Nature's Balance! Green Shuriken!"
Ash-Greninja gathered the red vines and turned them healthy green. They weaved them into the Green Shuriken, the purest form of their and Zygarde's shared power.
They flung it down into the earth far below.
The red vines dissolved and left a sparkly healing residue.
The townspeople of Lumiose City were amazed to find the destruction caused by the red vines repaired by a green mist.
The vines intertwined around Lumiose Tower disintegrated and left it back to the way it was before.
The murderous vine on the Tower's ledge disappeared and Clemont rose up from a sparkling green shower.
"What... happened?"
Ash-Greninja weaved Team Flare/Neo Flare into baskets of green vines. Including Lysandre.
Lysandre didn't know what to think. Ash-Greninja had saved him. And that was... beautiful.
"Pikapi!"
"You're back!" two voices shouted.
Ash-Greninja tied the final knot on the cages they'd weaved. Greninja nodded and Ash gave Clemont and Goh that dumb smile.
Then Ash-Greninja separated into boy and frog again.
And promptly fell asleep.
Footnotes: (1) Quote that Clemont frequently says in XY games and anime (2) Quote Clemont often says in the XY