"I don't understand…" Twilight said with a tremble in her voice, "These pokémon look just like ponies!"
Chrysalis nodded. "Indeed. We've theorized that all three of the tribes of ponies can trace their lineage to these pokémon. For years I studied the relationship between pony and pokémon, and what I found was shocking. You see, because pokémon can reproduce with other species, my theory is that pegasus, unicorn and earth pony all evolved at the same time from a common ancestor. Pegasi and unicorns have more shared genes with the Rapidash line, whereas earth ponies and donkeys share more in common with the Mudsdale line. We still don't have a solid hypothesis as to where Changelings came from, but we suspect the circumstances were similar.
The idea frightened Twilight. "So are we really just a special kind of Pokémon?"
Chrysalis shook her head. "As far as we know, no. If it were, you could capture a pony with a pokéball just like any other pokémon. Fortunately, that isn't the case. Although we do share a heritage with these pokémon, there seems to be something special that separates us from them. I hesitate to say it, but something magical."
Chrysalis led Twilight away from the pens and back into the Genesect lab. "You see, many years ago, ponies were much stronger than they are today. Unicorns had much more powerful magic, some supposedly strong enough to perform miracles. Pegasi had much stronger wings, and could keep up with powerful flying-types. Earth ponies were even hardier, and could pull heavy plows by themselves. Changelings too used to be able to transform their very appearance to disguise themselves as ponies. But as time passed, and ponykind started to live alongside pokémon, we no longer needed those powers, and as such, they evolved away. That being the case, we cannot trace any of those abilities to our pokémon ancestors."
"Then what gave ponies those powers?" Twilight asked eagerly. Chrysalis had just turned her entire perception of the world upside down, and now she desperately wanted answers.
"We aren't sure. It could have been an adaptation to compete with pokémon in our early years. It also could have been the work of mythical pokémon, although which one I could not say."
One more thing bothered at Twilight's mind. "So what happened to those pokémon? I've certainly never seen a Ponyta or a Mudsdale before."
"Owning them and using them in battle is strictly illegal for moral reasons." Chrysalis answered. "It would be like forcing your cousin to battle. They still live wild on a continent far to the south, which only scientists are allowed to visit."
"Oh." Twilight had nothing else to say. These pokémon still shook her deeply. She had never given much thought to where ponies had come from originally. For some reason, knowing that her ancestors were pokémon was deeply troubling.
Chrysalis led Twilight away from the lab, offering her a smile. "Thank you for coming to visit Twilight. It isn't too often I get to show off my work. Thank you for giving this old lady some time to brag."
Twilight smiled back. "It's my pleasure. I love being able to learn about new pokémon." Twilight looked at Chryalis again, focusing in on the old t-shirt peeking out from beneath her lab coat. "By the way, what is that pokémon on your shirt?"
"Oh this?" she asked, glancing downward at it, "This is Stufful. It's actually quite a common pokémon outside Equestria. If you cross the sea to Griffonstone, you'll find them everywhere."
Twilight pulled out her pokédex. A quick search confirmed Stufful wasn't listed anywhere.
"Let me see that," Chrysalis asked. The professor began looking through the options menu of the pokédex, checking the software installed on it. "Here's what's wrong. You only have an Equestria regional pokédex. I assume you'll be going to Griffonstone soon for a badge correct?"
"Yep." Twilight answered, "That's where I'll probably be going next."
Chrysalis nodded. "I would recommend visiting Cadence to upgrade this to a national pokédex before you leave. There's a huge number of pokémon that you might never have even heard of out there."
Chrysalis returned to the entrance of the lab, where Twilight's friends were waiting for her. Chrysalis gave the mares an approving nod. "Thank you for coming to visit. It was sincerely a pleasure to show you around. But I assume you aren't just here just to tour the lab, are you?"
Twilight shook her head. "No ma'am. I'm also here to challenge the Gym Leader here."
Chrysalis flashed a toothy grin. "As it would happen, you're in luck." She opened her coat, revealing a set of pokéballs hanging on the inside. I am the Gym Leader of Hive Omega, and I accept your-"
Danger, Danger! Intruders detected in Sectors 1, 4 and 6. Danger, Danger!
Alarms began ringing as an explosion rocked the underground laboratory. Chrysalis grit her teeth. Wordlessly, she turned on a computer monitor, looking to a security camera feed. "I knew it." She hissed. Twilight looked over Chrysalis' shoulder. Dozens of Team Umbra operatives were running through the halls, led by two officers in blue scarves.
"I worried this day would come." Chrysalis sighed. "We tried to keep Genesect a secret, but eventually somepony was going to find out." She turned to the six mares, a saddened look plastered on her face. "I'm sorry to ask this of you, but I don't know if my security forces can take care of this. You all seem like capable trainers, would you be willing to help protect the lab?"
"We'd love-" Twilight started, but was cut off by her friends.
"Come on out Luxio!" Rainbow Dash shouted.
"Phanpy, I need ya!" Applejack added.
Pinkie and Rarity followed up with Lombre and Zorua, and even Fluttershy produced her Buneary.
"Thank you, truly." Chrysalis smiled. She assumed a harsh glare. "Twilight, come with me, we need to secure Genesect. The rest of you, protect the lab. If their numbers become too great, use this key to lock the door." Chrysalis tossed Applejack a keycard, and took off with Twilight.
"Alright gang, let's show them Team Umbra bums who's boss!" Applejack declared.
"Right!"
Chrysalis and Twilight ran through the lab, dodging Team Umbra grunts and ducking through steel security doors as they closed. They kept up their pace until they reached the Genesect lab, which was empty save for the few scientists working there.
Chrysalis reached into her lab coat and took out two Pokéballs. "Heracross, Pinsir, I need you." Chrysalis whispered. Her two bug types came out, turning to face the shut door.
Twilight looked at her own pokéballs. "Cubone, Ivysaur, come on out."
They stood there with their pokémon, waiting for Team Umbra. After a few minutes, a reddish glow began pulsing through the door. After a moment, a pillar of fire briefly shot through. The door had been breached.
Two mares stepped through, both wearing the blue Admin scarves. Both of them immediately recognized Twilight, causing them no small amount of agitation.
"Long time no see, Sparkle." Sunset Shimmer growled.
"I must admit, I hadn't expected to see you here." Adagio added. "But no matter. We aren't here for you."
"Chrysalis, let's make this easy." Sunset continued. "Give us what we want and we'll leave your lab intact."
"Never. I'll never give my research to you cretins." She hissed.
Adagio sighed. "Very well then. I didn't want it to come to this, but you leave me no choice. Hitmontop, let's go!"
Chrysalis stepped forward with Heracross. With a sudden motion, she pointed her hoof at Adagio and her Hitmontop. "Aerial ace, go!" Heracross took wing, striking Hitmontop with a claw. Twilight was astonished my Heracross' monstrous strength. One hit and Hitmontop was already looking weakened.
"Triple kick, go!" Adagio roared in retaliation. Hitmontop lashed out with three kicks, each one more forceful than the last. Heracross guarded each strike, looking no worse for wear.
Chrysalis smiled. "Your Hitmontop is weak. Heracross, finish it with seismic toss!"
Heracross wrapped its arms around Hitmontop's body, holding it still while it flew into the air. Once it had reached the ceiling of the cavern, Heracross somersaulted midair, placing Hitmontop between it and the ground, and let them both fall. When they landed, Heracross smashed Hitmontop into the ground, leaving it embedded in the cement floor. Hitmontop was very much out of commission.
Anger radiated from Adagio. She had not expected to be defeated so easily. However, she calmly reached into her uniform and pulled out a Quick Ball. "Entei, crush these insects like the pests they are." She growled.
Entei burst forth from the ball, landing on the ground with a roar. Chrysalis quickly pulled Heracross back into his ball before allowing Pinsir to take his place.
"Still going to fight us with your bugs?" Sunset taunted. "A scientist of your renown should know to never use a bug-type against a fire-type."
Chrysalis' eyes were hidden behind a gleam on her glasses. "You'll find my bug pokémon to be more than you bargained for." Without another word, Chrysalis pressed her hoof up to the pendant on her neck. A bright aura began to emit from it and Pinsir, enveloping the pokémon in a blazing sphere of light. Twilight tried to process what was happening. It reminded her of seeing pokémon evolve, but this was something wholly new.
When the light faded and Pinsir became visible again, it had changed. It now sported a pair of wings and piercing yellow eyes.
Both Adagio and Sunset Shimmer were alarmed. "Sweet Celestia, did that disgusting thing just Mega Evolve?"
Mega Evolution? Twilight recalled back to the conversation she'd had with Cadence, asking her about the keystone. She had mentioned that Mega Evolution put a pokémon into a hyper-powerful state during battle. She looked onward in amazement. She had not known what to expect a Mega pokémon to look like, but Pinsir seemed to fit the bill perfectly.
"Entei, Flamethrower!" Adagio commanded.
"Dodge." Chrysalis calmly said back. Entei's mouth brimmed with flames, which it shot in a lancing beam toward Pinsir. But with its new wings, Pinsir easily moved out of the way. Chrysalis smiled. "Retaliate with double hit." Pinsir flew down to Entei, lashing out twice with its arms, striking it surprisingly hard.
That hit was incredible. Twilight had not expected Pinsir's attack to do as much damage as it had. Chrysalis chuckled, sensing Twilight's awe. "Twilight." She said, her attention never breaking from the battle before her, "When Pinsir Mega Evolves, its ability becomes Aerilate, which turns all of its normal-type moves to the flying-type. Mega Pinsir is also a flying-type, so all of his flying-type attacks become stronger as a result."
"Hey grandma, pay attention!" Adagio yelled. "Entei, hit them with an eruption!"
Entei began to loose huge spouts of fire, bathing the battlefield in flame. As evasive as he was, Pinsir was not able to dodge it all, and was quite obviously suffering.
"Pinsir," Chrysalis commanded, her calm voice having the slightest edge of annoyance in it. "Guillotine. Now." Pinsir flew at Entei at nauseating speed, its large pincers spread wide and ready to snap shut. It stopped the instant it reached Entei, snapping the massive mandibles shut with an audible crack. Entei fell over instantly, knocked out by the single hit.
Adagio's jaw dropped. "Inconceivable! How could my legendary pokémon lose!"
Sunset Shimmer sighed. "Typical Adagio. Allow me to show you how to handle a legendary pokémon." She held out her own pokéball, tossing it onto the ground. "Moltres, come forth!" Moltres emerged and spread its fiery wings, letting out a commanding cry.
Chrysalis turned to Twilight, speaking to her in a raspy whisper. "Twilight, I need you to grab my helmet." She commanded. "Once you get it, I need you to press the big red button on the computer console and type in the password 'Stufful'." Without a word, Twilight galloped off, grabbing the device and punching the password into the computer. As she returned the helmet to Chrysalis, a red alarm began to ring, allowing a prerecorded message of Chrysalis began to play.
Vault override command has been accepted. Genesect containment unit offline.
The walls to the containment cell holding Genesect were pulled down into the floor. Chrysalis smiled and put on her helmet. A flash emitted from the eyes of the helmet and then Genesect adopted a rigid stance. Twilight smiled. They're in for it now.
Genesect ran to Chrysalis' side, turning to fearlessly face Moltres. The light on its cannon cycled through colors until it settled on blue. Chrysalis smiled at her opponent. "If you want to fight legendary pokémon, I'm more than happy to oblige. This is Genesect, and it shall be your opponent."
Sunset Shimmer didn't waste any time. "Moltres, flamethrower!" She roared.
"Techno blast." Chrysalis ordered in response.
The two pokémon fired off their beams. To the surprise of everypony but Chrysalis, techno blast's watery beam began to push back against the flames. Surely enough, it was overpowering Moltres.
The spray hit Moltres like a fire hose, causing the legendary bird to shriek in pain. Huge amounts of steam rose off Moltres. The water-type attack had hit it like a train.
Sunset was visibly worried. Her pokémon, her legendary pokémon, was being beaten easily. The techno blast hit had been so powerful, Twilight suspected Moltres wouldn't be able to take another hit of that power.
Chrysalis wasn't going to take any more risks. "Shock wave, go." She grinned as a lance of lightning arced out of Genesect's cannon. Try as it might to evade, the surge followed, striking Moltres and knocking it out of the air.
While Chrysalis and Twilight dealt with the admins, Rainbow Dash, Applejack and the rest had their hooves full with a small army of Team Umbra grunts. They had set themselves up in a line, standing between the criminal gang and the tunnel that led down to where Twilight and Chrysalis had gone.
"Luxio, hit 'em with another thunder fang!" Rainbow shouted. Luxio sank its fangs into yet another Raticate, taking down another grunt and causing him to gallop back the way he'd come.
Applejack smiled to her as her Phanpy landed a clean rollout onto the opposing Bibarel. "How many you up to Rainbow Dash?"
"That one makes four!" She answered proudly.
"Heh, just finished six," Applejack bragged.
Rainbow Dash shot her a dirty look. "No fair, three of yours only had one pokémon."
While her friends continued to argue and battle, they remained oblivious to Fluttershy, who was visibly struggling. She was facing off against a Duskull, which continued to hit her with pursuit and will-o-wisps while all Buneary's normal and fighting type attacks couldn't hit it.
Finally, Rarity came to her rescue. "Zorua, bite!" Her dark-type sunk its teeth into the ghost, knocking it unconscious and allowing Fluttershy a brief respite. "Are you alright dear?"
Fluttershy sniffled, wiping away a tear from her eye. "No."
Rarity gave a sympathetic nod. "Very well. I say it's high time you and I depart. Rainbow Dash! Fluttershy and I are going to retire for now. Can you hold without us?"
"Hey, more for me!" She answered glibly. Rarity sighed. Luxio Phanpy and Lombre would be enough to hold the line for now. She led Fluttershy down the tunnel deeper into the lab. As they passed through another section of lab, they saw two familiar Team Umbra grunts throwing some mechanical parts into a sack.
"The boss is gonna give us a promotion for sure!" Panic Attack gleefully giggled.
Crimson Comet laughed in agreement. "That's for sure!" As they turned to leave, they saw the two mares, and froze.
"Crud!" Panic Attack groaned. "It's those twerps again!"
"Nah, those are the chumps. But if they're here, then that means the purple one and her friends gotta be here too." Crimson said. They looked at each other for a second.
"Retreat?" Panic suggested.
"Fine by me!" Crimson glibly agreed. Without another word, they galloped off, leaving Rarity and Fluttershy staring blankly.
"Well, they certainly can run fast." Rarity observed.
"'Let me show you how to handle a legendary pokémon.'" Adagio sarcastically remarked. "Yeah, you sure showed them."
"Oh be quiet!" Sunset Shimmer snapped. "The boss is going to have both our tails for this."
As the two commanders continued to argue, the radio in Adagio's pocket began to frantically buzz. She pulled out the transceiver and allowed the message to come through.
"Boss! We got the goods!" Crimson Comet declared triumphantly. "We're on our way to the rallying point."
"Copy that soldier." Adagio returned her attention to Chrysalis. "Well I'd love to stay and chat, but it seems we have business elsewhere. Sunset Shimmer, come." She took off with Sunset begrudgingly following.
Chrysalis sighed. She used her helmet to put Genesect back in its containment unit, before removing the device to address Twilight. "I'd feared this day would come for many years now. But now that it's passed, I am no longer afraid. Genesect has proven itself more than capable of protecting this facility."
"I'm glad everything turned out okay." Twilight smiled. "But what were they here for?"
Chrysalis pondered this for a moment. "I couldn't tell you. I had assumed they were after Genesect, but that doesn't seem to be the case. Unfortunately, they got whatever they were after. I'll have to figure that out for myself." She let out a long, relieved sigh. "At any rate, thank you Twilight Sparkle. Now, continuing where we left off earlier, as the Gym Leader of Hive Omega, I accept your challenge."
"I look forward to it." Twilight bowed.
Chrysalis didn't respond. She started looking off into space, pondering something. "Hmm…" She murmured. "Could she be the one..?"
"Pardon?"
Chrysalis snapped back to reality. "Excuse me. You see, I learned something important from that battle. You can run all the analyses on a pokémon you want, but you will learn far more through battling at their side. In short, I may have a task for you."
"What would that be?"
"Twilight, if you prove yourself worthy in our battle , I would ask you to train a pokémon for me. Like Genesect, I still don't know what it's capable of. I am tied to my research here. So I would ask that you train it, and see what its potential really is." Chysalis looked past Twilight, down the hall which housed all of her exhibits. "It deserves it."