Story of Villains: Queen Chrysalis

by Major League Gaming Trap

Rating: teen
Tags: Queen Chrysalis, Starswirl the Bearded, Princess Celestia, Tragedy, Discord, My Little Pony: Friendship is Magic, Dark, Death, King Sombra
Length: 5084

This is the story of the Queen of the Changelings and how she came to be.

Other villain stories can be found here.

This is a story that takes place before and after the findings of Equestria. Chrysalis was not always the evil Changeling Queen, she used to have a much happier life before Equestria was founded.

Note: This story does not take anything relating to the IDW Comics. While there may be some things that were originally from there, they aren’t treated the same way.

Published 2024-10-06 14:40:00 UTC
Last updated 2024-10-06 14:40:00 UTC

The Story

Author's Note

Note: This story does not take anything relating to the IDW Comics. While there may be some things that were originally from there, they aren’t treated the same way.

The Story

Long ago, the realm of Skyros was the home of the Alicorns. These all-powerful beings were the combination of the Pegasi, Unicorn, and Earth Pony tribes. This tribe was hidden away from all ponies. The only tribe that knew of their location was the Flutter-Ponies.

Chrysalis was the Alicorn of Nature. She was a tall Alicorn with green skin, green eyes, a dark purple mane and tail, and her cutie mark was a ladybug with leaves.

While she was a kind pony, giving plants and crops to the other Alicorns, deep down, she had darkness in her heart. She had always wanted world domination. However, thanks to the kindness she was getting from the other Alicorns, she had that balance that kept her from letting the darkness turn her evil… For now.

She was also both jealous and impressed with Celestia, who was a young filly at the time. She was capable of controlling the Sun, which made her quite popular. Chrysalis and Celestia have chatted with each other on many occasions.

One day, Celestia told her, “I am so happy. I have a baby sister!”

Chrysalis was surprised and said, “Congratulations! What’s her name?”

Celestia says, “Her name is Luna. Mom says that she will be capable of moving the moon some day.”

Chrysalis was impressed. She had always dreamed of having children and seeing what they could become. Chrysalis would occasionally visit Celestia and Luna’s home to watch over them while their parents went out.

One day, Celestia noticed Chrysalis was opening a portal. She ran over to her and asked, “Chrysalis. Where are you going?”

Chrysalis turned her head to Celestia and told her, “I’m going to visit the Flutter-Ponies.”

Celestia then asked, “How come?”

“They relayed to me a message that they were in need of my help. Don’t worry.” She patted Celestia on the head. “I’ll be back soon.”

She smiled at her and Celestia blushed. The two then embraced each other in a hug. The hug ended and Chrysalis walked through the portal to Flutter-Valley, home of the Flutter-Ponies.

The Flutter-Ponies were like Pegasi, only with butterfly wings. They had magic that rivaled even the most powerful unicorns at the time. They were also hidden away from the tribes. Chrysalis loved this tribe more than anything. She had a very deep connection with them and treated them like family.

The Flutter-Ponies were currently dealing with two dark dragon-like creatures. They had crystals all over their bodies, yellow eyes, and no pupils. Chrysalis arrived and witnessed the battle going on, even seeing one of them get swatted away with its tail.

She flew up to them. It was Rosedust, the leader of the Flutter-Ponies. She has a light yellow coat, a light pink mane and tail, light pink eyes, and a light blue bow on her tail.

“What is going on here? What are those things?” Chrysalis asked.

“We don’t know. They just showed up here and one of them keeps telling us that this is for their father.” Rosedust answered.

Chrysalis then asked, “Do you have any ideas on how to stop them?”

Rosedust nodded her head no. Chrysalis then looked up at the battle. Then she noticed something off. One of the dragons had tears in their eyes. Almost as if they didn’t want to do this.

Chrysalis then used her royal voice while also casting a bubble around the two dragons, “Listen to me, my friends! I have a plan!”

The bubble wasn’t going to last long, however. The Flutter-Ponies heard this and then flew over to Chrysalis to listen in.

She told them, “I noticed something off about one of those dragons. One of them doesn't seem to want to hurt, but something is forcing it to. Using your love magic, you could purify it.”

They all nodded in agreement to this plan. The bubble popped, and the Crystallized Dragons charged at Chrysalis and the Flutter-Ponies. The Flutter-Ponies start pouring all of their love into the Crystallized Dragon, while Chrysalis is handling the other one. Their plan has worked as it turned the Crystallized Dragon light blue and gained dark blue pupils.

Meanwhile, Chrysalis was being beaten by the Dark Crystallized Dragon. It was way more powerful than she had realized. The Dark Crystallized Dragon had Chrysalis within his claws. Before he could eat her, the Light Crystallized Dragon blasted the Dark Crystallized Dragon in the stomach with his blue fire breath, which caused him to drop Chrysalis.

The Dark Crystallized Dragon looked at his brother and yelled out, “How dare you?! You have betrayed our father and master! For that, you must be destroyed you traitor!”

The Light Crystallized Dragon said back, “I’d rather perish with honor than continue this meaningless slaughter!”

The two Crystallized Dragons engage in battle, flying all around the place and firing at each other. Eventually, they open a portal that leads somewhere. They fly through, continuing their battle, and the portal closes.

The Flutter-Ponies started celebrating alongside Chrysalis. This celebration was cut short however when multiple portals opened up around them and they were ambushed by a bunch of mutated animal fusion creatures that outnumbered all of them. Every Flutter-Pony was crying and screaming out in pain as they were stabbed, blown up, and blasted away. Chrysalis lasted the longest but was stabbed through the back.

She falls to the ground and, before her eyes close, she hears someone say in a dark low raspy voice, “Pathetic” and sees the hoofs of a large, dark blue ram.

Chrysalis started to wake up all of a sudden. When she opened her eyes, she saw a dark Unicorn, King Cobalt, in front of her. She spoke, “What the? what happened? Who are you?”

Cobalt stepped forward to her, “To put things simply, I brought you back to life and with new forms and powers.”

He summoned a mirror and she looked at herself. She stepped back in horror and then looked at what used to be the Flutter-Ponies. She then turned back to Cobalt in anger.

Her horn glowed and she said, “WHAT HAVE YOU DONE TO US!”

Cobalt said without the smile leaving his face, “Like I said Chrysalis, I brought you back to life and with new forms and powers.”

“BUT WHY AND HOW DO YOU KNOW MY NAME!” Chrysalis yelled.

Cobalt then said, “I read your mind. I also want you to help me and I will give you what you want in return.”

The glow from Chrysalis’ horn started to go away. “What makes you think we would ever help you?”

Cobalt said back, “Because I have the power to also take your lives away again.”

The anger left Chrysalis’ face and she said, “Fine! What do you want?”

The dark magic of Cobalt had started to reignite the darkness in Chrysalis’ heart. Only this time, much more powerful and it fully engulfed her. She is now a creature that is beyond redemption.

The smile on Cobalt’s face grew even bigger, “That’s more like it. Also, call me… Sombra.”

Sombra then tells her, “Now listen here before we attack. I made you all into creatures that can change their form any way you and your fellow children wish. Yes, these are your children now. You can reproduce them without a male. Destroying the harmonious world is fun, but I must admit that messing with ponies in other ways besides destruction like with their minds and health is much more entertaining.”

Chrysalis felt the dark magic within her and it felt nice to her. The feeling inside of her body pulsed with it and it was amazing.

Sombra then tells her, “Now let's see you all transform.”

He recreates the mirror and Chrysalis focuses on the power and she turns into her original form.

Sombra yells out, “Perfect! But I am afraid you can’t keep your old form.”

With the glow of his magic, Chrysalis turns back to her new form. She is now unable to turn back to her original self. Chrysalis’ muscles tightened as she felt rage, but remembering that he could take away her life again, she just decided to do nothing.

Sombra continues, “Also, you can feed off of all emotions, but the one that you should feed on the most is love for both power and food.”

Chrysalis says, “Alright, can we just get moving already?”

“Of course. Here’s the plan.” Sombra then tells her what to do while also telling her the tale of the Windigo’s and how Equestria came to be.

In the Capital Building, there was a room where the Founders of Equestria stayed. Commander Hurricane, Princess Platinum, and Chancellor Puddinghead all sat in the three highest seats. They no longer kept their old titles. Their subordinates sat next to them, the ones who began the bonds of friendship that united them.

They were discussing the disappearance of Cobalt. “My friends,” Platinum began, addressing everypony, “I know I’ve been saying this a lot, but I miss my father.” Clover the Clever wrapped around Platinum in a big hug. They both blushed at this.

Clover reassures, “It’s going to be okay, we’ll find him one day. Just keep holding on to hope.”

Suddenly, laughter filled the chambers, causing all present to pause and look around in confusion. Chuckling, the figure of the now Queen Chrysalis stood in the entryway, her mouth in a cruel grin. “You must be the Founders of this Equestria as you call it. You exceed my expectations. I was expecting something else.”

The ponies were shocked to see this thing. They had no idea what it was, but it clearly gave off a dark vibe. Hurricane was the first to speak up, “What are you?”

Chrysalis stepped forward a little, then said, “I am Chrysalis, Queen of the Changelings, and I am here to bring you all to King Sombra so he can execute all of you.”

Everypony was shocked to hear this and they took a fighting stance. “Not a chance, lady!” said Puddinghead.

“You will do no such thing!” said Platinum.

Queen Chrysalis just laughed at this display and then said, “Alright, my children, they chose the hard way!” The ponies were confused by what she meant by 'children'. Until a group of Changelings appeared from out of nowhere and tackled them.

The doors to Sombra’s new throne room burst open and the Changelings walked through carrying the Founders of Equestria. They tossed them in front of him. Sombra stood up from his throne and walked down to the ponies before him.

He then looks up at Chrysalis and says, “You have done well. Now you’re free to do as you please.”

Chrysalis then has an evil grin and says, “Excellent! Let's go and attack all the ponies, my children!” With that, the Changelings left the castle and started their attack on Equestria.

They wreaked havoc and destruction among all the ponies, even feeding off of the love they had. There were also a few deaths. Just then, a blast of magic flew toward Queen Chrysalis. She manages to dodge it before it hits her. She looked down to see Star Swirl the Bearded.

Chrysalis then laughs and says, “Oh please! An old little horse thinks they can mess with me. I’m sure Sombra is going to love seeing your body by his hoofs.”

With that, she charges at him, but before she can hit him, he teleports out of the way and behind her. He hits her with another magical blast, which sends her flying into the forest. The changelings see this and go to protect their queen.

Chrysalis and Star Swirl were locked in battle, firing magic at each other and knocking each other back with their own hooves. Their fight seemed even until the rest of the Changeling race jumped in and Star Swirl was having a harder time.

“Hehehe. Not so easy when it’s just a hundred against one is it?” Chrysalis boasts.

Star Swirl slowly gets up and says, “Not yet.”

His horn glows and he releases his magic. Chrysalis defended herself, but the magic wrapped around her and the other Changelings. They all are now trapped in a giant orb of light. Star Swirl moves it and traps them all in a tree. Star Swirl took a few breaths.

He then says, “They’re finally defeated. Now to deal with the king!” He then makes his way to the castle of the dark Alicorn King.

Years have passed, and the tree that Star Swirl had trapped the Changelings in had started to grow and morph.

As it turned out, that tree was grown over the heart of the Dark Crystallized Dragon’s grave site. The Light Crystallized Dragon had won the battle but was very injured. As it made its way through the mountains of the north, they succumbed to their injuries and passed on. That mountain had now become the Crystalling Mountain.

The tree started cracking and eventually, Chrysalis freed herself alongside the other Changelings. They all swarmed around the tree, which had grown into a castle-like structure. They could feel magic radiating off of it. This was coming from the thrown, which used to be the Dark Crystallized Dragon’s heart.

Queen Chrysalis then says, “All right my children! Now that we are free, it’s time we take over Equestria! And seeing as Sombra is no longer around as it seems, we don’t have to worry about him taking away our new lives!”

The Changelings roar out in joy. Chrysalis started to laugh maniacally. Their stomachs start to grumble. They remember that they need to feed off the emotions, especially the love, of others so they can survive and gain more power. Chrysalis and the Changelings soon began attacking many kingdoms and civilians. Chrysalis at one point even turns a group of small, peaceful, and adorable cat-like creatures into black stains on the ground.

The Changeling Kingdom, as they call the morphed tree, became their home where they lived for many years. They try their best to stay under the radar so that no one can stop them. They also are taking in as much love as possible so that they can become so powerful that no one will ever stand in their way again. During their time in the castle, Chrysalis also started to give birth to new Changelings. She was a little grossed out by that, but she didn’t mind as she was now a bug-like creature.

On day, in the woods, Queen Chrysalis was scavenging the area when she came across an amalgamation of different creatures looking over the horizon.

“What is that thing?”, she thought to herself.

She started to approach the creature. He turned his head hearing the rustling in the bushes. The two were now looking at each other face to face.

The creature spoke, “Oh, why hello there.” He appeared behind her, “I’m Discord the Draconequus. Who might you be?”

Chrysalis jumped away from Discord in shock. She answered, “Chrysalis, Queen of the Changelings, and I have never heard of a Draconequus!”

Discord responded, “That’s because I am the only one of my kind.”

Chrysalis looked skeptical, “Right… What even are you doing up here all alone?”

Discord grabbed her, carried her to the ledge, placed her down, and pointed to the site, “Well, I have just been watching this interesting-looking party going on down there.”

Chrysalis then questioned, “Okay… Why aren’t you down there enjoying the show?”

Discord gave her a glass of chocolate milk. She took it in her magic with a confused look. He told her, “Try it. It’s delicious chocolate milk.”

Chrysalis took a little sip and enjoyed it, not as much as love but she liked the taste of something physical.
Discord then told her, “Also, to answer your question, it should be obvious why I’m not down there. Not everypony would accept the way I look.”

“True. I do question how you are doing all of this weirdness like making a glass of this chocolate milk appear.” Chrysalis started to question.

She looked at him to see him now eating cotton candy with chocolate dripping out of it. He tells her, “To put it simply, I have the powers of chaos. I can do whatever I want, whenever I want.”

Upon hearing that explanation, an idea came into her head. She didn’t think this freak was completely intelligent, so she could take advantage of him.

Chrysalis then said, “Interesting. If you could do all of this, how about you improve that little party down there?”

Discord looked at her interested. “I’m listening.”

Chrysalis smiled as her plan started to work. She pointed to a float that was a wood carving of Princess Celestia. “Let's take a look at some of those floats there. They don’t look right with the color brown. Wouldn’t you say?”

“Well, yeah, they don’t look all that colorful.”

“Exactly. Can you change the color to… let's see… pink?”

Discord stroked his beard, “Hmmm… Now that you mentioned it, you're right.”

He snaps his lion's paw and the carving of Celestia turns completely pink. Everypony was surprised upon seeing this.

Chrysalis continued, “Perfect! Now how about some confetti? Don’t parties have it?”

“Well, I haven’t been to one of these before. Do they?”

“Well, they should.”

“Well, if you say so.”

He snapped his lion's paw again and 12-foot-long confetti started to rain all over the ponies. Even a bunch of Pegasi got caught in it. As their wings got caught, they started to fall from the skies. Now everypony was getting more freaked out.

Chrysalis clapped her hooves at this display. “Excellent! Now there is one more thing that would make this such a banger.”

“And what would that be?” Discord started to get a sinister grin as he loved the chaos down there.

“Think you could make it rain that chocolate milk you gave me?”

“Hey, you’re right! That would be a banger. Here it goes.”

With a wave of his paw and claw, he summons a bunch of cotton candy clouds over the town, and is started raining chocolate milk. Everypony was now screaming and running all around the place in fear.

Discord and Queen Chrysalis were now laughing at the display going on down there. Discord says, “This is really fun! Why haven’t I thought of this sooner?”

“You just needed the right push.” Chrysalis turned around and started to leave.

Discord saw her leaving and asked, “Hey, where are you going? The fun has just started.”

Chrysalis stopped in her tracks, turns her head 180 degrees, and says “Why would I stay? I gave you what you needed. You have the power to take over Equestria easily. You should use that opportunity. Besides, I have a family to feed. I’ll be back soon.” She then turns her head back forward and left.

She returns home and tells her children, “Listen up! I have given us an opportunity to obtain an immense amount of food and power! Follow me.”

They all started to make their move.

When they reached their location, they could see how much chaos was going on. This shocked even Queen Chrysalis, but she snapped out of it and they started their attack. Once more, they terrorized the populous. Things were different as ponies were flying all around the place.

Queen Chrysalis was taking the love away from a newborn filly until she heard the evil laugh of someone familiar. She turned around to see Discord upside down, staring right at her.

Discord then says, “How nice seeing you again. Like what I’ve done with the place?”

“Indeed. It does look nice.”

“And it seems you’ve brought your children. This works perfectly for me.”

He then appeared right beside her with his lion's arm wrapped around her. Discord summons cupcakes. Chrysalis tried it and loved them. The two then started laughing together at the mayhem and chaos going on in Equestria.

They both suddenly heard a commotion outside. They look to see Princesses Celestia and Luna fighting off the Changelings. Chrysalis flew out of the house they were in and charged at the two sisters. Celestia puts up a shield to block the attack. The two looked at each other, realizing who they were.

Celestia spoke up, “Chrysalis, is that you?”

Chrysalis backed away a little. “Well now. Celestia has fully grown up. How lovely.”

“What has happened to you?” Celestia asked with tears in her eyes.

Chrysalis spoke up. “This is the new me. Chrysalis, Queen of the Changelings!”

Celestia didn’t know what to do. On one hoof, this was one of the ponies who she loved for her whole life since she was a filly, but on the other hoof, she was clearly not the same pony she remembered. She wasn’t even a pony anymore.

“Chrysalis, don’t you remember all the fun times we had? All the laughs we shared? Why are you doing all of this?”

Chrysalis just stood there, saying nothing for a while.

Eventually, her horn glows as she shouts out, “Those days are over! I am no longer weak and innocent! I am a queen, and I will take over Equestria! No matter what.”

She fired an energy blast at Princess Celestia. Princesses Luna gets in the way and fires back.

Luna looks back at Celestia and says, “Sister! Whoever the Chrysalis you knew was is gone now! We need to fight back!”
Celestia, still with tears in her eyes, understood what she had to do and joined in the magical struggle. They push back Chrysalis, but she charges back in and they engage in battle. Chrysalis shows off her shape-shifting abilities which prove to be quite a challenge for the two sisters

Discord was just sitting in the house watching everything go down. He then said, “Oooh, drama. That is lovely.”

Celestia and Luna then put their horns together and they fire a magical spell that they used on a centaur long ago. Chrysalis is swept up in the magic and she is trapped in Tartarus. She is also put in stone to make sure she doesn’t escape. They also make sure that she is far away from the other prisoner so that they wouldn’t steal her magic. All the Changelings were also swept up and trapped in a faraway mountain.

The Changelings were all defeated. Celestia was still in tears with Luna hugging her to help her calm down.

Discord clapped his hands together. “Bravo little princesses. You’ve defeated a group of bugs. Including their queen who believed she could manipulate me.” An idea then popped into Discord’s head, “Ooh. I should wright that down just in case I need to use it.”

The royal sisters get ready to battle the Lord of Chaos. But that’s a story for a different time.

Aftermath

Author's Note

All the events mentioned here happen within their canon episodes. This part gives more context for some of them, going into what happens during them.

Aftermath

After a thousand years, the spell had worn off. Chrysalis was no longer a statue. She looked around and noticed she wasn’t in Equestria anymore. She took off, flying around the place. She sees a giant dog with three heads.

“Well isn’t that a hideous creature.” she thought to herself.

She then sees the exit. The dog was guarding it. Chrysalis flew toward the dog and transformed into a dragon and breathed fire at it. The dog got out of the way quickly, but was than slapped by her tail. Chrysalis turned back to her normal self.

She hears someone call out, “How did you do that? What are you?”

She turned her head around to see a small and old centaur-like creature chained to the ground.

“All you need to know is that I am a Changeling.”

The dog got back up and was charging at her. She turns into a bird and flies all around the three headed dog making him dizzy. She then flies to the door turning back. Using her magic, she opens them and escapes. The dog chases after her, but soon loses her. He also loses his way back to Tartarus and finds himself in Ponyville.

Meanwhile, Chrysalis tries to sense for her children’s presence. She finds them within a mountain. Using her magic, she breaks open the mountain and frees her children. They all managed to return to their home undetected. Chrysalis started birthing new Changelings to make sure she had as large of an army as possible.

Queen Chrysalis leaves the hive to find good places to steal love from. She finds herself going to Canterlot. She sees a big, white Unicorn with a shield cutie mark holding a ring in his magic being shown to a pink Alicorn with a heart cutie mark.

Chrysalis could feel the love radiating off of both of them. She then has a plan. She returns to the hive and tells her children about the plan.

She creates a threat against Canterlot, which causes Princess Celestia to have Shining Armor remain in the city. He puts up a magical protective bubble around it. None of them realize that Chrysalis made it through.

Shining Armor and Princess Cadance start to get things ready for the wedding. Cadance was in her room getting prepared when she heard a laugh. She looks behind her to see herself. Before she could say or do anything, the imposter’s horn glowed a sickly green and she was blasted in the face knocking her over.

Then green fire started surrounded Princess Cadance. She screamed and cried for help, but her doppelganger merely laughed at her misery. The flames enveloped her, and in a flash she was gone, sent to the the caves below Canterlot.

“Time for the next stage of this plan. That Shining’s love would give me more power than I could possibly even dream of having,” she said to herself.

She went to the bridesmaids and them to ensure that Cadance wouldn't escape the caves before going to meet Shining Armor. She saw how his little sister, Twilight Sparkle, had raised her suspicions, but she didn’t pay much mind. She was able to convince Twilight's friends and family that she was innocent, leading them to turn against Twilight. To make sure that her plans don’t fail, she also traps her in the caves with Cadance.

Although they escape and ruin the wedding, they were too late and Chrysalis had gained the power to defeat Princess Celestia and makes Shining Armor lower the bubble so her children can feed. However, as we all know, Shining Armor and Princess Cadance’s is able to defeat them and the Changelings are blasted out of Canterlot.

After they regroup in the Changeling hive, Queen Chrysalis starts expressing her anger that their plan failed. Over time, as she’s trying to think of a new plan, she starts to lose lots of her care for her children. She has her children spy on the ponies, and she learns that Sombra was destroyed, Discord has changed his ways, and Tirek was sent back to Tartarus. When she hears that one of her children, Thorax, is a traitor, she didn’t even care. Then, she came up with a new plan.

They all manage to sneak attack and capture the Mane 6, Spike, Princess Celestia, Luna, Cadance, Shining Armor, and Flurry Heart and haves her Changelings pretend to be them. Thorax then teams up with Starlight, Trixie, and Discord to rescue them.

Chrysalis’ plan once more fails as Thorax shares his love with her and caused all the other Changelings to change their ways and share love as well. Because they did this, the throne was destroyed along with the old hive and the Changelings no longer had the fear of Sombra taking their lives away. Chrysalis refuses to change and voles revenge on Starlight and flies away.

She creates evil clones of the Mane 6 in order to control the Elements of Harmony and make a new hive. However, they try to betray her and use the Elements for their own ends, the Tree of Harmony recognizes them as fake and destroys them. With her plans ruined, Chrysalis swears vengeance upon Starlight Glimmer once again and leaves the Everfree Forest.

She tries to create clones of her old children as she didn’t have enough food to create more children. Before she could create them, she gets transported to a secret lair where she sees the centaur from Tartarus and recognizes it as Tirek. He was also with a little filly named Cozy Glow. When Sombra reappears before her, she is taken aback, but she doesn’t fear him taking away her life. When Grogar arrived, although she knew who Grogar was, she didn’t realize he was the one to kill her.

With the news that King Sombra was killed yet again, Chrysalis was both happy and scared.

Though at first, she didn’t want to bother with teaming up with anyone, after they retrieve Grogar’s Bewitching Bell, she saw an opportunity to take back control and accept the team up. She also comes up with the plan to betray Grogar.

To make sure that friendship isn’t used against them, she brings back the hatred of the different tribes. The plan was all coming together, with her getting the chance to defeat Starlight and all of Twilight’s friends. She would like to torture them rather than kill them like what Cozy Glow wanted to do. Upon seeing the Windigo’s return, she wants to let them turn Equestria into a frozen wasteland. In the back of her mind, she wants the ponies to be frozen and let whatever ones are left so they can be praised. In the end, friendship still defeats them and they are all turned to stone. This ends the tale of the Changeling Queen.

However, in an alternate timeline, Queen Chrysalis and her Changelings have taken over most of Equestria. There are only a few ponies hiding from the Changelings and they’ve become much more hostile towards strangers. This battle is still going on and no one knows who will win.