"I don't have the strength to repel them!" said Shining Armor.
"My love will give you strength," said Princess Cadance.
"What a lovely but absolutely ridiculous sentiment!" said Queen Chrysalis.
Using the power of their love, Shining Armor and Princess Cadance unleashed a magic explosion, which didn't affect the ponies but blasted Chrysalis out of the castle. All the other changelings were affected by the blast too.
Thorax was sent flying, but not nearly as far as the other changelings, recovering easily with his wings. So, he survived the attack, and the other changelings probably would too, but he had seen how the Mane 6 were fighting together, and the power of their friendship, and didn't want to be a part of Chrysalis's evil plans anymore.
He flew away, unaware that his less sinister personality had made him resistant to the blast.
Chrysalis, meanwhile, flailed her hooves helplessly. She was unable to use her wings due to the force of the blast, it having affected her the most due to her dark and sadistic personality.
She was flying horizontally in the direction of the Badlands, but before long, she began to fall vertically. Her only thoughts were of vengeance against Shining Armor and Princess Cadance. Then, she hit the ground with a THUD, and lay still.
The other changelings had been scattered in all directions. One of them happened to fall through a small hole in the middle of the forest and land in a pool of water. He climbed out, and looked around. This must be the Mirror Pool that he had heard about.
He was sure lucky he had landed where he did, or else he'd be dead. A lot of other changelings might not be as lucky, including their queen. So, he took off in search of fellow survivors.
He searched for days, and eventually came across one other changeling, who had landed on a Hydra in Froggy Bottom Bogg, and had made a hasty retreat as soon as he could flap his wings again. They decided that it would be best to return to the changeling kingdom, as other surviving changelings were likely to do.
Upon arrival at the changeling kingdom, they found three more changelings. Two of them had landed in water, and one of them had landed in a soft spot of dirt. They waited another week, during which two changelings came back, one having smashed into a wall in Cloudsdale, and the other having landed on a trampoline. After the week, the seven changelings decided that they were the only survivors.
"What about Queen Chrysalis?" said one of the changelings.
"I fear the worst for her," said another changeling.
"Let's go out and look for her!" said the first changeling, the one that had landed in the Mirror Pool. "We'll split up and search Equestria, disguised as pegasi. We'll meet up back here in another week."
A week later, the changelings hadn't found Chrysalis yet.
"Does anyone remember which direction she flew in?" said a changeling.
Five changelings shook their heads.
"I think I saw her flying in the direction of the Badlands," said the seventh changeling.
So the seven changelings flew out and searched the Badlands. Within the day, they found Chrysalis's body.
"The queen is dead," said one of the changelings.
"Not for long!" said the first changeling. "The rest of you, take a piece of her hair and take it back to our kingdom! I'll go get something that can make her reborn!"
One of the changelings pulled a hair from Chrysalis's tail. While the six changelings flew back to the kingdom, the seventh found a container, returned to the Mirror Pool, took a sample of water, and flew back to the kingdom.
Some time later, Pinkie Pie found the Mirror Pool and used it to create clones of herself - but that's another story.
"We'll put this hair in a chrysalis with some water from the Mirror Pool, and use our magic with it," said the first changeling. "If I'm right, it will create a perfect clone of her! Our queen will return!"
"Why don't we just throw her body through the Mirror Pool?" said another changeling.
"Because, the clone would be hollow and nothing like the original," said the first changeling. "This way, the clone will be exactly like her in every way, and maybe even retain her memories, up until her death. It'll be like reviving her!"
So, the seven changelings formed a chrysalis with their green changeling slime, and put the Chrysalis hair and Mirror Pool water inside it. Then they cast a spell on the chrysalis.
"How long is this gonna take?" said a changeling.
"Who knows?" said the first changeling.
A month later, the Chrysalis clone was completed, and opened her eyes. "I live!" she said. The last thing she remembered was taking a fall over the edge of Canterlot. She was unaware that there was another Chrysalis lying dead in the Badlands, and whose soul was imprisoned in a cage in the depths of Tartarus suffering endless nightmares.
She used her magic to make the cocoon disappear, and stepped out, shaking the changeling slime off her.
The seven changelings bowed to her.
"Where are my other changelings?" said Chrysalis.
"We're all that's left," said the first changeling.
"I'll need an army for our next attack!" said Chrysalis. "I must spawn more changelings! Once they're ready, you seven will take the forms of Twilight Sparkle and her friends! Which of you figured out how to bring me back?"
"I did," said the first changeling.
"Then you will take the form of Twilight," said Chrysalis.
And so Chrysalis spawned more changelings, and once they were big enough, she sent some of them to keep an eye on Equestria, disguised as background ponies. One of which took Applejack's form, mistaking her for a background pony, but nearly got discovered by Rarity and avoided taking her form from then on.
They learned that the Elements of Harmony were gone, but the Mane 6 had a new power, Rainbow Power, which they had used to defeat the all-powerful Tirek, and that Twilight Sparkle had become Princess of Friendship and got her own castle. Shining Armor and Princess Cadance now ruled the Crystal Empire and had a baby, Princess Flurry Heart.
"All right," said Chrysalis one day. "The time has come! You seven!" She pointed a hoof at the seven changelings who had "revived" her. "It is your job to replace Princess Twilight and her friends!"
The seven changelings flew away.
"I also want the other princesses, and Shining Armor!" said Chrysalis. "Bring them here and replace them! This time, Equestria is mine!" She began to sing This Day Aria again.
Author's Note
Yes, I know it's out there, and both officially and as far as the ponies know, Chrysalis in ACW and TWABA are one and the same. This is just my headcanon, and a possible temporary solution until such a time as the show decides to kill or reform her. (But then, there are other theories like Aria Blaze and Starlight Glimmer being one and the same)
The idea of a clone that retains all the memories of their original was inspired by the film The 6th Day, where the villains repeatedly die and get cloned, but retaining their memories makes it seem more like revival.
