Prologe
A long time ago, before Chrysalis invaded The Crystal Empire...
"Chrysalis, good to see you again" said King Sombra in Queen Chrysalis' throne room "What do you want?" asked Queen Chrysalis asurtivly. "I mearly wish to negotiate" answered King Sombra winking at her. Chrysalis caught on to what he was getting at, but usually she's the one doing the seducing. "Leave us" ordered Queen Chrysalis. Knowing all to well what was about to go down, they left without question and began preparing the egg sacks. 'Fool' thought King Sombra as he took a step toward Chrysalis. However when she bagan to spread her legs, King Sombra used telekinesis to grab her by the neck and began choking her. Unable to speak, Queen Chrysalis tried to cast a spell but discovered, she couldn't use magic. "But... how?" choked Queen Chrysalis. "How are you unable to use magic ageinst me? Simple, I know my crystals" said King Sombra as he threw her on the ground, releasing her of his magic. *cough*cough*cough!wheeze!* "See this Ruby atop my crown? It's the Ruby of Backfire. With it, whatever enchantment you may have over your kingdom won't affect me, but will affect you. For example, since your throne only allows changeling magic, it now allows any magic except changeling magic" answered King Sombra. "But...why?" asked Queen Chrysalis now trembling in fear. "Why? Oh come now Chrysalis, do I really need a reason to kill you? Nice and slow" answered King Sombra as he began torturing her. "AAAAAAHHHHHHH!!!" screamed Queen Chrysalis as she woke from her trance. "It was just a vision! Why you! I'm going to-" yelled Queen Chrysalis as she suddenly stoped, realizing her magic wasn't working. She then yelled in surprise "WHAT?!? But it was just a-" "A vision?" said King Sombra as he took a step toward her. Queen Chrysalis, now trembling in fear took a step back with her head down. "Don't dismiss everything you see in a vision. Most of what I said was true, I do have the Ruby of Backfire with me. But I won't kill you, not if you cooporate" said King Sombra. Queen Chrysalis began to cry, never being so scared in her life, she cried. Sombra backed her up ageinst a wall, and to her surprise gave her his cape and held her close. "There there, I won't show you my cruel side, if you cooporate" said King Sombra in a calming tone. Queen Chrysalis, now trembling less asked "What do you want from me?" "I want you and your army" answered King Sombra. "My army? But why?" asked Queen Chrysalis as she pulled away from Sombra "Because I think we can benefit from eachother" explained Sombra. "My army is currently trapped in the prison beneath The Crystal Empire. I need your army to free my people" explained Sombra, "What's your plan? Go in and take over? Don't you think we've tried that before!?! We have to get on the inside!" yelled Queen Chrysalis. After realizing what she just did, she went back to trembling. "I...I..." stuttered Queen Chrysalis in fear. "Your meticulous planning is admired. One of the many reasons why I need you cooporate" said King Sombra glaring at her. "Your right, I'm sorry. I shouldn't have yelled" admitted Chrysalis submissvely, afraid of what he might do. Sombra grinned and said "It's quite allright, I understand your frustration. Now, what is your plan?" Chrysalis answered with "My spies have reported their princess is getting married in in a few months. We kidnap and imprison Cadence in her own dungeon, where your army is being held, I take her place brainwash Shining Armor and-" "Shining Armor, hmm. Twilight will stop you" said Sombra "I know, as I was trying to explain, we imprison her along with Cadence, she will escape and supposedly 'save' the day" explained Queen Chrysalis. "If you know it will fail, why go fourth with it?" asked Sombra. "Because the goal is not to take over The Crystal Empire, not yet. That prison is impenetrable, however knowing Twilight and her past deeds, she might be able to escape. Weakening the prison, allowing us to later free them, and take over" explained Queen Chrysalis. "Then after they're free, we take over all of Equestria!" proclaimed Sombra. "Uh, we?" aksed Chrysalis "Yes, with our armies combined, I will take Equestria by force!" proclaimed Sombra. "When will you let me go?" asked Chrysalis unsure if she wanted to know. "My dear Chrysalis, if I let you go, who would be my queen? No, once Equestria is mine, you will be ruling by my side. This is and alliance after all, is it not?" persuaded Sombra. 'I'm not sure if I want to be your queen, but I don't think I have much choice' thought Queen Chrysalis. "Yes, I suppose it is. I should go ahead and give the order. It takes awhile to fully brainwhash a pony after all" replied Chrysalis.
That being said, Queen Chrysalis took Princess Cadence's form. Twilight exposed her at the same time doing exactly what Sombra wanted, to weaken the prison.
Ok, now let me take a minute to explain the science behind Changlings(Which I totally made up). The chances of a female Changeling being hatched are 15% out of 100. That being said the chances of a male Changeling being hatched are 85%. Furthermore, it is very natural for Changelings to lay up to one, thousand eggs per, therefore Chrysalis has layed the eggs of every Changeling in her Kingdom. Due to this, on the rare occasions a female Changeling is hatched, she is the official Princess of the Changelings, and is taught how to rule and her duty of producing offspring. It's simply how the Changelings survive, thereby making it tradition to serve no king, but only serve the Queen. Also, it takes three years for a changeling to fully develope inside an egg sack. (PS: due to this, Changelings are extremly loyal to their queen. That being said I did not include Thorax at all in this story, because I came up with the basic outline before they even made up Thorax. He would just simply jepardize everything)
Three years have passed with Chrysalis carefully spying on Princess Cadence, afraid for her life doing exactly what Sombra wanted. Then a pleasent surprise quickly turned to ruin. "Queen Chrysalis! An heir has hatched!" reported Buzzer, Captain of the Changeling guard. "Really? I finally have a daughter? Which brood?" asked Chrysalis with hope in her voice. "Brood 929 my Queen" replied Captain Buzzer, "Then she's half pony" commented Queen Chrysalis. "Yes your Majesty, we allready incased her in the Transformation Chamber to alter her pony DNA" said Buzzer. "Ahh, Good! The last thing we need is a weak ruler. Escort me to her!" demanded Chrysalis "Yes my Queen! Right this way" obeyed Buzzer. Buzzer led Chrysalis to the Transformation Chamber, where the hybrids and prisoners were all incased in egg sacks to make them 100% Changeling. "Her sack number is 108 my Queen. Hear she is" said Buzzer. Upon Looking at her daughter, her eyes lit up with glee, and for the first time love. "She's beutiful" said Chrysalis as she began to cry. "Yes my Queen, she is. If I may ask, what shall her name be?" asked Buzzer, "Cocoon, Princess Cocoon" answered Queen Chrysalis. "A fine choice my Queen" complimented Buzzer as he to, began to cry.
Later that evening, Sombra was doing his usual check-up with Chrysalis, to make sure nothing would get in his way. "Word around The Hive is that 'an heir' has hatched. Is this true?" asked Sombra. Queen Chrysalis, to happy to keep it in, exclaimed "Oh yes! It's simply the most marvelous thing that's ever happened! I finally have a-" "She has to die" inturrupted Sombra. "Wh-what? Why?" asked Chrysalis in surprise. "She'll get in the way of everything I've worked for" replied Sombra, Chrysalis was shocked, and tried to reason with him "Bu-but, It's how our kind survive! You can't-" "Do you dare question me?" asked Sombra in an angry tone as he glared at her, silently warning her not to push him. As scared as Chrysalis was, she was not about to kill her own daughter, as she said "Maybe, Sombra just hear me out-" "I. Don't. Care. Either you will kill her, or I will" demanded Sombra. Chrysalis was speechless, "You have an hour to decide. After that, I'll kill her, nice and slow" threatened Sombra as he walked away. Chrysalis, couldn't take it. As she began to cry, she ran to her chambers to sob in privacy. After she had left however, Buzzer who had been disguised as a rock, changed back to his true self, saying "I knew he couldn't be trusted, I have to warn everyone!" he then flew as fast as he could, then came at a sudden stop, as he realized. "The best choice of action would be to report to the Captain of the Guard, which is me" said Buzzer as he slowly fluttered back to the ground with his head down. "What to do Buzzer, think, analyze, decide. Hmm, there isn't enough time to let the whole hive know, Sombra is using the Queen's worst fear against her, what should I do?" asked Buzzer to himself as he was contemplating the situation. Then he had an idea as he told himself "I don't have a choice, the princess' life is in danger. I have to take her to the father, I have to go to The Crystal Empire"
To be continued...